Saturday, June 27, 2015

Inside Cell Block 7

Signs all over said leave your cell phone in the car, so I have no photographic evidence, but we spent our morning at the Cell Block 7 Prison Museum near Jackson, Michigan. It’s a working state correctional facility but they operate a museum in an unused wing. You can visit the prison yard, see the cells and the place where they eat, look at an exhibit of confiscated weapons, everything.

It was especially interesting to talk to a former guard, a retired guy who likes to spend his Saturdays volunteering as a docent.  He says that although the guards were outnumbered about 80 to one, they typically walk through the prison and interact one-on-one with prisoners and after working there a while, the inmates and guards become pretty friendly with one another.  The New York prison escape is in the news, so we asked and he says it can only have been possible if there was widespread corruption among the staff. All the other prisoners must have known the details of the escape while it was being planned. It’s just a thing among prisoners that they all get to know one another, there are no secrets, and there are no snitches.

Yes, homosexual activity is extremely common. Especially if you’re a young, white man, he says, you will certainly be a target, and you may as well just get used to it. In the showers, in the laundry room — the guards just can’t watch everyone all the time. The prisoners repeat over and over that they’re not gay, it's just something they all need to do.

You should have see the clever weapons and other confiscated contraband.  Plenty of sharpened screwdrivers, spoons, scissors, etc, but other things too: one guy even made a working set of walkie-talkies. Some of the prisoners had TV sets in their cells, which apparently is completely okay as long as it was purchased in the prison store.

From the upper level of the museum cell block, you could look out over the entire facility and see current inmates walking to and fro. I think Michigan must be fairly progressive in its policies (they banned capital punishment in 1846) because the prisoners are all kept busy, on everything from making license plates to growing trees. They have one big rule, though: no prisoner can earn money or be assigned a non-cleanup job, unless they pass their GED.

It feels good to be tough on crime, to think it’s okay for prisons to be cruel places where they get what they deserve, but you need to remember that many of these inmates are fundamentally good people who just made a mistake.  I imagine what it must be like to have your own son or brother in jail, and how you’d want the place to be fair to him. Sixty percent of those who are released end up coming back to prison, partly because there are so few things they can legally do on the outside. Many of them study for business degrees, intending to start their own businesses, like landscaping or home repair. Many of them end up in food service, as cooks, waiters, dish washers, etc.

Cell Block Seven Logo

Friday, June 26, 2015

Overselling the microbiome

Here’s the cover of a magazine I saw yesterday in the grocery store checkout lane:

 Tabloid cover on microbes

I thought about submitting it to Jonathan Eisen's list of Overselling the Microbiome, but sadly, I don’t think it would make the cut. These types of articles are becoming too common to deserve an award.

There is surprisingly little that is known about the microbiome, and for every study that shows some connection between this or that microbe and this or that condition, there are counter-examples galore. Some of it is a measurement issue: even if you do sample a person’s microbiome, are you sure it’s a representative sample? Studies of gut microbes are nearly always made on the organisms that exit the body, so by definition any measurement is of something that is no longer bioactive.

I’m interested in the microbiome because I think the whole subject is incredibly fascinating, and I believe that eventually science will find some deep insights that will radically alter the way we think about what it means to be human. I hold out hope that we may find a few tricks to manipulate the microbiome in some specific cases, and certainly in general it is good to learn more about how our bodies work. 

But c’mon people, tone it down a little.

Thursday, June 25, 2015

Which species do I track?

At the Microbiome breakout during last week’s Quantified Self Conference, several people were interested in the list of organisms I track.

Here’s the list, along with my own results for the past seven samples: 

MayJunOctJanFeb21-Apr28-Apr 
Akkermansia3.10%1.97%0.76%0.63%NA1.16%0.95%genus
Bifidobacteria Longum0.00%NA0.19%0.96%0.21%0.05%0.00%species
Bifidobacterium0.85%0.65%5.87%6.65%0.69%0.71%0.00%genus
Christensenella0.03%NA0.00%0.00%NA0.01%0.01%genus
Christensenellaceae8.26%3.97%4.03%4.10%1.35%0.00%0.00%family
Faecalibacterium prausnitzii9.96%6.23%0.58%9.54%13.64%10.64%16.56%species
Roseburia1.36%1.12%0.78%4.28%1.08%0.80%4.94%genus

Why this particular list? I’ll be honest: no particularly strong reasons. Most of these are derived from various conversations with the super-knowledgable Grace Liu, now based at The Gut Institute.  I strongly encourage you to follow her there, and on twitter @gut_goddess for better information.

Note: after speaking more with experts at uBiome and elsewhere, I’ve concluded that it’s okay to trust the species information for many of the organisms, including the ones above. Although 16S rRNA is not very reliable at detecting anything below the genus level in general, there are some organisms where the genus is the relevant species. Sure, I suppose it’s theoretically possible that another species may exist as part of that genus, but in reality none has been found in humans.

Also note: even the word “species” doesn’t mean the same thing for bacteria that it means when speaking of lifeforms like humans that reproduce sexually. After all, bacteria reproduce by simply dividing in half. There is no concept of of a “species divide” like that one that prevents a dog, for example, from reproducing with a cat. There is plenty of gene transfer and gene mixing that occurs among bacteria, but that often (perhaps usually) crosses the lines of what we might think of as unique species.

The bottom line: don’t get too hung up on a particular species. If something is biologically active, it may not matter whether you’re tracking at the genus level or the species level. Well, maybe it matters, but for most purposes you won’t get any closer by knowing the species name. In some ways, knowing that something is a member of a particular species can give you a false sense of confidence, when in reality science knows far less about the activities of these organisms than we would all hope.

Do you have any specific organisms that you like to track?

 

 

 

Wednesday, June 24, 2015

Fact-checking should be a business

By tradition and by default, books aren’t verified to anything near the standard of a magazine piece.
I am continually amazed at how often mainstream, otherwise trust-worthy news sources get things wrong.  As the quip goes, “I find that the New York Times is always right, except in areas where I have first-hand knowledge.”  Even peer-reviewed scientific journals are not immune: only about 40% of results published in top-tier psychology science journals can be fully replicated.

There are plenty of everyday examples:
  • Medical and health information is notoriously inaccurate, even from sources you’d hope you can trust. For decades, the Center for Science in the Public Interest, as well as the National Academy of Sciences, encouraged the American public to eat trans-fats.
  • A quote regularly repeated by New York Times op-ed author David Brooks, about a rising sense of self-importance among American adolescents appears to be entirely wrong. 
  • Many, many books have been retracted, or published with disclaimers
What if there were an organization, like UL (that approves electrical equipment) or Consumer Reports (that recommends a variety of household products), only instead of dealing in physical goods, they put their stamp on books or magazines?  Of course we already have book reviews, often by people who are themselves experts in the subject, but how many of them go systematically through all the facts and references to be sure that every claim in the book is accurate?

Cochrane is one independent organization that tries to be systematic in its reviews of the trustworthiness of medical findings.  Verificationist is a service that offers to do fact-checking for books on behalf of publishers or authors. Morningstar and many other investment advisory firms do this for stocks and bonds. Can’t we get something similar for books?

Unfortunately I think this would be a lousy business. Too few publishers or authors would be willing to pay to have their own work fact-checked, and most customers, if given a choice, would prefer a cheaper book with facts presented in “good faith” over a more expensive one that was independently vetted.
Francis Bacon What is Truth

Tuesday, June 23, 2015

[book] Epidemic of Absence

Ecosystems go all the way up and all the way down. Just as humans affect -- and are affected -- by the bigger world of animals, forests, oceans, and sky, we are also part of a deeper micro-sized world of bacteria and viruses, many (most?) of them far older than we are, and constantly adapting to all the harshness of life, including the new realities of human-made antibiotics and hygiene. Control over nature is an old goal of science, but nature is never fooled forever. The great bridges and dams that make one side of our lives better can have unforeseen consequences to other parts of our world. 

So it is with the micro world too. Even the simplest steps we take to keep clean or warm, conveniences like indoor plumbing or heating, induce changes to unseen world of microbes, which not only outnumber us but out-class us in diversity and complexity. Eliminate one from our lives and who knows what it will do.
 
Moises Velasquez-Manoff presents an intriguing and sometimes terrifying survey of what little is known about the microbes around us. Focusing on allergies and autoimmune diseases, he writes in detail about the "hygiene hypothesis", that as the world gets richer and cleaner, our under stimulated immune systems get bored and turn on the body itself. A whole range of new diseases, from hay fever to asthma to crohn's disease, all seem to co-occur with modernity. People of the same genetics and culture -- Finns separated by the Iron Curtain, for example -- suffer these diseases at very different rates. Even zoo animals develop afflictions unknown in the wild.  The more "clean" and "modern" you are, the more you invite previously unheard of conditions. 
 
Even more intriguing is the "old friends" hypothesis, that having co-evolved with us, many of these microbes are actually necessary for health. From digestion to mood, when you take away the organisms that have covered us for millions of years, you invite trouble. Sadly, by driving many of these creatures to extinction -- an inadvertent result of hygiene practices intended to wipe out other afflictions -- we may be adversely affecting our human ecosystem in ways we don't yet understand. Wipe out a wolf population to spare human livestock and the deer begin to trample wild plants, carving the forest in unpredictable directions. There is some good, of course, but some bad too, and the scary part is that science doesn't know way too little about which is which.
 
I am extremely fortunate to have been spared many of the awful afflictions presented in this book: hay fever, peanut allergies, asthma, eczema and more. So little is known about how to treat the sometimes terrible discomforts involved, and if you suffer from them, you may understandably be willing to try just about anything, including treatments with parasites like hookworm, so mainly you want to know: does it work?  The answer is maybe, but not definitely, and you may also introduce other problems. The author recounts how he self-inflicted in a Tijuana clinic (sadly, the treatment is illegal in the US) and yes, it helped. But the side effects (headache, diarrhea) were no picnic, and the treatment is no cure: to maintain relief from allergies, he needs to continue taking the worms. With no independent auditors in place, you run the risk of acquiring other diseases along with the worms: HIV maybe or hepatitis -- the cure can be worse than the disease.  
 
This definitely was one of the best science books I've read in a long time, and if you or a loved one suffers from autoimmune diseases, you'll appreciate the well-written and thorough survey of what is known. I doubt there is any work nearly as good; I think this is one of those areas of science that is so new, and so potentially different from centuries of medical progress, that you really need somebody like this author -- not a scientist, but a science journalist -- to look into the issues and present them for you (which he does, well, and with the right amount of both optimism and skepticism).
 
A sampling of some ideas:  how pregnancy is central to the passing of important microbes.  Yes, you should lick your baby's pacifier, and chew their food for them if you can -- the microbes in your saliva are highly optimized for your genes and environment.  Even autism may have a microbe component: some kids reverse their symptoms when fighting a fever, or an infection. H. pylori, the strange bug whose role in ulcers earned its discoverers a Nobel prize, may actually be necessary in many of us.  
 
In fact, the lesson of h. pylori or the EVB virus is a good summary of many of the bugs around us: often they are neither all good nor all bad. Nature is not a fight between pure good and pure evil, but rather a constant tension among multiple constituencies vying for power. Rather than focus on permanently vanquishing one or another "foe", we need to consider the entire ecosystem and realize how little we really know after all. 

Monday, June 22, 2015

What I learned at Quantified Self 2015

I’m back from two jam-packed days at the QS15 (the Quantified Self Conference) held at Fort Mason, in San Francisco, and I have a few impressions.

There were three “cool” new ideas that I thought played an outsize role at this conference:

1. All things Microbiome

(obviously I would think so). uBiome was there, including an appearance at the first day’s plenary by Jessica Richman. My tweet (and heavily retweeted) summary of the session was a quote from the first speaker: “We are the last generation without personalized medical data”. That’s true for the microbiome especially, and it was wonderful talking with so many people about their new bacterial experiments.  I’ll write more in future posts.

2. Heart Rate Variability

With better technology for measuring heart rates, many people have noticed that pulse/minute is a less useful measure than variability. Sometimes it’s more meaningful to look at how much each heart wave length varies from the others: high variability tends to be associated with creativity or improved mental processing, whereas low variability tends to be accompanied by stress or low learning situations. 

Paul LaFontaine used HRV measurements to demonstrate that he is more nervous in situations involving presentations to groups of people than he is in situations reporting to a superior. Mark Leavitt showed it as a way to measure willpower. 

3.  Direct Cranial Stimulation

I thought this was fringe stuff when I first heard of it a few years ago, but enough people have tried it that I’m starting to rethink my skepticism. JD Leadam even has a company, https://thebrainstimulator.net/ selling devices for a little over $100.

Other

I was especially impressed by a breakout session led by Evian Gordon (http://mybrainsolutions.com) who seemed to know a ton about every imaginable aspect of assessing mental performance. Anyone interested in Seth’s Brain Tracker would want to understand what those guys are doing as well. Daniel Gartenberg  is another psychology expert in attendance who I knows a lot about this subject. I had good results beta-testing an app he wrote that claims to help with deep sleep, so it was nice to talk with him in person again. 

What I didn’t see: Apple Watch.  Oh sure, there were some discussions of HealthKit and ResearchKit, but unlike QS15, which seemed to be attended by a significant percentage of the world’s Google Glass wearing population, I saw very few Apple Watches. Whether this is because the availability is still so limited or whether the QS early adopters just haven’t taken to the Watch yet — I don’t know.

I’m expecting that http://quantifiedself.com  will dish out many more details in upcoming days and weeks. Worth watching further.

Quantified Self Conference 2015

Thursday, June 11, 2015

Zocdoc vs OpenTable

The idea behind ZocDoc is brilliant: a modern, super-easy web site that lets you book a doctor appointment as easily as OpenTable lets you book restaurant reservations. ZocDoc knows each doctor’s specialties, which ones take which insurance plans, their location, and — the best part — which times are available for appointments. Go to one web site, enter your information, and immediately doctors in your neighborhood that meet your requirements. Find one you like, book the appointment, and that’s it!

That’s what’s supposed to happen, but unfortunately the inanity of the American healthcare system gets in the way, and today was the second time I’ve been unhappily surprised at the results.

The front end works fine. I entered my information and quickly found a list of doctors in my area that meet my requirements, including availability times. I hit submit and that was it: a nice, professional confirmation for a visit with a doctor with good reviews. They even added the appointment automatically to my iPhone calendar, and offered to text me a reminder before the visit. ZocDoc already knows my insurance and basic health information, so I didn’t even need to fill out additional forms for the visit. Perfect!

Unfortunately, that’s as far as the resemblance to OpenTable restaurant reservations ends.  I had scheduled my appointment for 1pm, right after lunch in the area close to where I knew I was going, but early on the day of the appointment I received an odd email from a different doctor confirming my appointment for 11am. The ZocDoc site knew nothing about this, so I called the new doctor to see what was happening.

The new doctor’s receptionist was confused too. From her point of view, I had made an appointment at 11am. If I didn’t show up on time, or if I canceled the appointment less than 24 hours beforehand, she would charge me a fee. The fact that I had booked it through ZocDoc — and that I had a different time confirmed — was not relevant to her.

Well, I shifted things around so that I was able to make the 11am appointment, but frustratingly, when I arrived I had to fill in all the forms (again). A cheerful physician’s assistant brought me into the exam room, took my vital signs and then, almost as a side comment, warned that my insurance company probably wouldn’t reimburse me for today’s visit.  What!?

By then, it was really too late for me to get up and walk out the door. The doctor arrived, I had my brief appointment (I wanted somebody to look at a suspicious mole) and that was it. No problems, I’m fine.

Later, at the original ZocDoc appointment time, I received that promised text message reminding me of my visit and helpfully offering to give me additional support if I reply with the message ’s’.  I did, and talked with a very kind, helpful ZocDoc representative who assured me that they do everything possible to ensure that I have a good experience, blah blah blah.

This is turning into a long rant and I appreciate, dear reader, your indulgence as I get this off my chest. But it occurs to me that ZocDoc is in a business that is fundamentally so different from OpenTable, that it may be impossible to give me a good experience. Unlike OpenTable, ZocDoc’s “customers” (physicians pay them a flat monthly fee to be listed on the site) already have too many IT systems. From insurance and Medicaid reimbursement to government-mandated certification, HIPAA, and reporting requirements, their staff is probably just too busy to deal with yet another web site. Solving that “last-mile” problem with the receptionists would require much more training and hand-holding than ZocDoc can afford.

Eventually all of this will be sorted out and sometime in the future doctors will join the 20th century IT revolution just like every other industry, but it will be a long time. If you want high-tech, don’t go to the doctor: go to a restaurant.
ZocDoc logo