Turn Your Head and Cough


So I went to the doctor today to get a checkup, and told him about the project – he’s doing a super duper blood workup to give me data.  He pointed  out that lipid numbers tend to increase during the holidays (duh!) and so might want to do another draw in the spring if they seem high.  Never heard a doctor suggest that before!

He also said something about that ritual that all men go through.   Since we were boys, we’ve been told to turn our head and cough, while the doctor puts his fingers oh so firmly in a very private spot, feeling for a hernia.   So I asked, why do I turn my head and cough?  His reply was that when you cough, if there is a weak spot in the abdominal wall, he’ll feel it, and can detect a hernia in the making.  Fair enough.  But why turn your head?

“So you don’t cough all over the doctor.”

I had no idea! All these years I thought there was some clinical reason for the head turn.  Next time, I’ll just cover my mouth.

Oh, and below is my EKG reading.  He said it was normal.  I’ll take his word for it since I have no idea what I am looking at.

My EKG 12/21/11 (click for full size image)


Open Data and Body Parts: A Cautionary Tale

1 Comment

Bone ScanI have a story to tell you about collecting your own medical data and why it is increasingly important for us to demand and understand our own data.  But I’ll cut to the punchline and then fill in the details:

@xenijardin:  So, if anyone ever asks why having a copy of your medical data, and viewing it, is a good thing? You may now refer them to my #ghostpenis tale.

Did I get your attention?  So what is this all about?

Xeni Jardin is a technologist and influential blogger for the geeky blog BoingBoing.   She often writes about how technology, and in particular social networks, has influenced major events in society.  She has written in depth about the role of Twitter in political uprisings around the MidEast and she was all over the Occupy movement before any of us were.

I follow her on Twitter – she is wickedly funny and seems to have a pulse on the tech community.  But a few weeks ago, she announced on Twitter that she has breast cancer.  One of the strange things about this new social networked world is the amount of sympathy that you can have for people you have never spoken to or met.    Words of encouragement poured in.   She wrote up her story for her blog: she was compelled to go get a mammogram after friends had been diagnosed.  The powerful story of her diagnosis is worth a read.

Being a proponent of open technology and personal rights, and just outright curious, she asked for the data from one of her body scans.  The lab gave it to her, in three CDs.  The data was in bits and pieces, in bunches of files, and in weird formats.  Xeni gave a shout out to friends on Twitter, who helped her find the tools to take a look at her scans.  That is when things got weird.  Here are the key tweets:

@Xeni: So I figure out how to open my bone scan data. I look. WTF. What’s that dick-shaped ghost-shadow thing—it looks like I have a penis! [1/2]

@Xeni: I agonize about it all day. Do I have a hidden penis hanging out in my leg? Can female parts or colons look dick-shaped on bone scans? 2/3

@Xeni: I call a hacker pal. “That, Xeni, is a dick.” Look at metadata more carefully. THEY GAVE ME THE WRONG DATA. SOME OTHER DUDE’S SCANS. 3/3

At first, this might seem like a harmless mixup.  But Xeni starts to wonder:   Did the doctor I just spoke with, who was giving me my prognosis *read the wrong scan*?   And if so, where is my data?  Who has access to the images of my body?  Is this an honest screw up, or evidence of gross incompetence on the hand of people I have trusted with life and death issues? These are serious issues, and issues that she would have been totally unaware of if she did not request her data.

I had something similar happen once.  Once I called the doctor for some test results, and the doctor told me that my pap smear came back normal.  Now this might be because my wife and I have freakishly similar names, or maybe I dont have the deepest voice.   But really???  And what if my pap smear wasn’t normal? What would they have told me?

Xeni’s story is still being written, and a good writeup of the issues involved (including Xeni’s twitter feed) can be found at e-patients.net.  It’s pretty riveting, and despite the underlying seriousness, even funny at times.   It made me aware of a medical information movement, called Give Me My Damn Data, which advocates for patients’ access to data.  I’m going to make sure to keep my eyes on it.

This is important stuff.  We need more information about our health information to make informed decisions about our health care (and, as Xeni found out, to keep an eye on the system).   We can get access to our purchases from Amazon going back 10 years.   But try and get access to all of your medical data from that time?  It’s near impossible.   But imagine if we all had access to our data, we could learn so much from ourselves, and others out there.  It is already starting with sites like patientslikeme.com.

There are other interesting aspects to Xeni’s story which relate to My Year of Data.  By opening her private details up to the internet community and Twitter, she was able to a) get help in actually accessing and understanding the data b) get emotional support from friends, c) get legal advice about the issues involved, d) solicit suggestions on how to deal with the situation, and e) create public pressure on the caregivers involved to fix the problem (or at least get her the correct data).

So, I’ll say it again:  Give Me My Damn Data.

Seth Roberts and Citizen Science


alt butter

Last year at a statistical meeting I met Seth Roberts, a psychology professor at Berkeley and at a Tsinghua University in Beijing. I had been following his blog for a while, and found him to be a fascinating writer, so I was looking forward to the talk. He delivered one of the most interesting hours of entertainment you can imagine at a statistics conference.

Seth has devoted countless time and energy to self-measurement and understanding. He has been monitoring and recording data about himself for many years, mostly to learn about how his daily practices and his diet impact his life. He has discovered many interesting things about himself this way:

  • The best way he found to lose weight is to eat “flavorless calories” between meals – calorie dense but bland things like extra light olive oil. He found that this lowered his ‘set point’ and caused him to get full faster when eating, ultimately lowering weight. He wrote a book about it, called the Shangri-La Diet. It is a bizarre concept, a diet which does not actually restrict eating, but instead encourages eating empty calories between meals.
  • He discovered that eating half a stick of butter per day improves his brain function, as measured on a standardized test of simple arithmetic questions that he takes every day. (He has made R code available for his daily math test)
  • He has found that eating pork fat helps him sleep better.
  • Fermented foods are essential for good health and blames the lack of fermented foods in American cooking as a reason for our general poor health and obesity.
  • Eating breakfast makes him wake up earlier – skip breakfast and sleep longer and better.
  • Sunlight exposure during the day helps him sleep better
  • Standing on one leg until exhausted has a huge impact in helping him sleep better (you might have guessed that he has sleep issues)

His paper covers a lot of the above topics. These ideas are all somewhat derided by the mainstream as not having any real ‘science’ behind them.

Which brings us back to the talk at the statistics conference. He covered a lot of the above material and discussed how many of the discoveries were stumbled upon accidentally. But by taking good records of his diet and his sleep and his emotions he was able, after many years, to look at the data and see the correlations. He went beyond this and claimed that he was sure that these results were not just valid for him, but for humans in general. Butter does not make him sleep better. Butter makes humans sleep better. There is no way that he could see such a strong effect and have this not be due to some biological process. He didnt know what that process was, but he was 100% sure it was true.

That was the fun part. He said this to a room of biostatisticians who are ingrained with the dogma of the scientific method and well-designed clinical trials being the only way to really understand biological effects like these. Seth was telling them to take their sample sizes and fancy randomization and shove it. He knows these things to be true because they happened to him.

The incredulous response of the biostat crowd turned to indignation and rejection pretty fast. But he kept pushing, saying isnt it possible that I know my body well enough to know that this must be true? And the effect is so strong that it cannot only be true for Seth Roberts’ body? Don’t human beings have core similarities?

More importantly, he had an important message for science: Imagine if thousands of people did experiments on themselves and kept copious notes on themselves. Imagine if all of these notes were shared and the community allowed to analyze the data. Imagine how much we could learn about diseases like cancer by running thousands of concurrent experiments around the world. Today, running a proper clinical trial requires doctors, biostatistians, and federal regulators, and costs millions of dollars over several years to do one experiment. Seth estimates he does about 200 experiments on himself a year, and estimates the cost at a few hundred dollars. Which is the more efficient model?

The fury in the room was palpable. Most dismissed him out of hand. But is it so crazy? We are starting to see patient led, crowdsourced learning through clever sites such as Patients Like Me. Others say this movement of ‘citizen science’ is the wave of the future. As a statistician, I know that we will still need to use good practices to collect and analyze data, understand variance, correct for biases, and assess significance. But perhaps we need to be a bit less dogmatic and listen more to people like Seth.

My new toy


Today in the mail I received my new toy, a Withings scale:


I got it courtesy of my employer, who is doing an employee based health devices trial ( more on that in another post if I get permission.. )

The scale is super cool. It measures weight ( duh ) and is networked into my home wifi to automatically download weight to my profile to make pretty charts and stuff. It can also auto detect who is standing on it ( assuming the members of the family are sufficiently different) and chart each person separately.

But the cool thing is that it measures body fat %. It does this apparently by injecting me with a tiny electrical impulse. Here’s my first reading:


19.3% ??! !? I have no idea if this is good or bad but to me it sounds bad. I’m 20% fat? A quick online search tells me this is ‘acceptable’. I’m not so sure.

Anyway I’m supposed to measure this in the morning before a meal and I did just the opposite. Plus, online reviews are skeptical about the accuracy of this device. My wife says the only way to measure fat properly is by being submerged in water. That sounds like fun! Anyway, even if the number isn’t accurate, hopefully any trends will be noticeable. Data coming soon!!

Tracking Happiness

1 Comment

It seems clear to me as I take my trip through tracking my health, my weight, and my activity for a year that one of the things that will impact how successful I am is my attitude.   Obviously moods change from day to day, and I am kind of interested in how it changes, and how those changes effect the other things that I am tracking.  Will being in a good mood help me stay on track with my health goals?  Will staying on track with my health goals improve my mood?  How does my attitude change with the trends I’ll observe in diet, sleep, exercise, work, etc?    I’m really excited to try and find out, but the question remains:

How do you track happiness?

It’s difficult to think about recording your feelings in the morning in the same way you might record your weight.  It just doesnt work.  “Hey, I feel really 74 out of 100 today!!”  Emotions are too multi-dimensional to score in a single number.

As it turns out, there are people out there who have tried to do exactly that.  One I have been trying for the last week or so is called Moodscope. Moodscope is a cute little website designed to help you track your feelings on a given day.  They ask you to answer 20 questions a day: each question is a feeling (like ‘inspired’, ‘angry’, or ‘joyful’), and you answer whether you feel it not at all, a little, quite a bit, or extremely.   The interface is a card that you flip around until your answer is at the top and then click it:

It’s fun the first time or two, but honestly can get a bit tedious after that.  The data entry takes about 3 times as long as it should due to the cutesy card interface, and often try to ‘trick’ you by asking two of the same questions in a group of 20 (I know that is a way to assess data quality , but it feels like either trickery or incompetence to me).

Anyway, they add up your 20 answers into a single score (your moodscope, I guess).  Typically, everything I felt was either ‘a little’ or ‘not at all’ (I tend not to get too irritable or enthusiastic first thing in the morning) and my score is hovering around 50.  It feels unsatisfactory and arbitrary.  I doubt I will keep up with this.

So what other options are there?   It is interesting to me to think about where Moodscope fails (for me).  They send me an email in the morning to answer these questions, but mood changes throughout the day.  I think more effective would be a tool that sends me a text at random times assessing my attitude.  Something I can reply to super fast, with a minimum amount of effort.  That might be useful.    I’ll keep looking.

This woman (8 minute video) came up with her own system.  She rates mood on a scale of 1 to 5 (same as Netflix, but backward! :):

It’s hard to see, but her scale is pretty funny as described:

1: Great.  Over-the-moon, birthday cake  and unicorns exist

2: Good.  Fresh lemonade and sunshine.

3. Neither. Meh.

4. Bad. Nothing is funny.  Grey skies.

5. Horrid.  Lost the winning ticket and ice cream doesn’t exist.

She records her mood on this scale 3 times a day 5 hours apart, all on post-it notes, by programming her cell phone to alarm her.  The post-it also recorded what she was doing at that time.  She correlated it with other things she was doing, like interacting with friends, family or taking public transit.  She seemed to learn quite a bit about herself, and she credits the mood tracking with helping her to make some important life decisions like her career path, her relationships and which train to take!   I recommend the video, she comes across as really convincing and kind of sweet.  She says she has an iPhone app but I couldn’t find it in the App Store.  I’d definitely try it out!

Finally, I’ll leave you with a fun little project I read about while researching this:  a building in Berlin that tries to read the mood of the people passing the building and display it as a smiley or frowny face.  There is scant detail on the ‘science’ they are using, but it makes for a great visual:


I am not alone

Leave a comment

Did you ever have what you thought was a great, original idea, only to find out that lots of people had already come up with a similar one?

I felt that way a little bit last week, when doing a little research for an upcoming blog post on tracking happiness I came across some people, no, actually an entire community of people who are doing exactly what I am doing.  Yes, there is an entire self-tracking community out there!   They have blogs, and meet-ups, and even conferences.   Wow.

The center of all of this activity appears to be at the Quantified Self web site.  Go ahead and feel free to take some time over there.  I’ll be here when you come back.

OK. I spent quite some time over there and was amazed at all of the stories I read – people who have tracked data about themselves for years.  Most of the stories are about health, or weight, but some focus around tracking emotions, or sleep, or productivity, or happiness.  Also, some fascinating videos of presentations from previous QS conferences.

So, like any research project, I need to do a bit of a review of the existing material.  I’ll share some of that material from QS and other  resources as I uncover it and think it is relevant to my project.   And ultimately, I shouldn’t feel bad about not being original – I mean, if others have the same idea, maybe it is not so crazy! 🙂

Calorie Me


Tracking caloric intake is probably the most significant way to really, seriously, take on any effort to lose weight.    Logging everything that you eat in a day is a very enlightening experience.  For me, I realize how often I want to grab a snack, look in the refrigerator just because I happen to walk past it, or open the snack cabinet just because I am bored.   Another culprit is when I eat what is left on my kids’ plates, on the way from the table to the sink.  It’s easy to ramp up the calories without even being aware of it.

Here is a prime example of my Uncertainty Principle (see my first post if you dont know what I am talking about).  The fact that I am measuring this stuff, the fact that I know I have to write it down, makes me less likely to do it.   The effect here is strong, much stronger than I realized, at least in this first week of my experiment.  At work last week someone was walking by with a plate of cookies that were left over after a meeting.  Now, I NEVER pass up a plate of cookies.  EVER.  In fact, previously I would have been likely to grab one, and then try and find out where the tray ended up to go grab another later.   But this time I thought ‘well, if I take one I am going to have to whip out my phone and record it.  Is it really worth it for  a Trader Joe’s chocolate chip dipper?’ (answer: no).

Living healthy is the result of HUNDREDS of little decisions that are made during the day.  Take the cookie?   Take the stairs?  Go for a walk after lunch?  Pass on the extra portion?  Choose whole wheat bread?  It is very easy to make the wrong decision for any one of these little decisions, and rationalize it away as just being one little decision.   The powerful part is that when you make a few healthful choices, there is inertia to help you make more.

Anyway, back to calorie logging.  I am finding it is a very effective way to be mindful of my eating choices.   So that is great.  The problem is, it is a big pain in the rump roast.  There is no easy way to do this.  Thank goodness we live in a world of technology  where there are endless people trying to build apps to do it for me.    In a perfect world, these apps would allow me to take a picture of what I am eating and it just records all the nutritional info.  Alas, the world is not that easy yet.

I’ve been trying out three apps that let me do this:  the Fitbit app, which is tied into my wonderful new Fitbit tracking device; the Livestrong MyPlate app from Lance Armstrong’s health juggernaut; and a popular one called LoseIt! – which is tied in with their weight loss website.    All of these websites have a similar vibe, you search for a food product in their databases which have thousands of food types in there.  If you find what you ate, you just click “I Ate This” and it logs it for you.

Easy, right?  Well, its easy if you ate a package of Mac and Cheese, where the nutritional info is right on the box and easily downloadable.  But what about my wife’s delicious lentil soup?  Or my bean stew from the other night?   Or a homemade chef salad with diced ham and cheese on top?   Unless you are measuring your ingredients to the 1/4 cup and logging every one, it is extremely hard to figure out what you have just ate.

Here is a screen shot from the Livestrong MyPlate app.  I typed in Chef Salad – it immediately returns about 20 different options, including store and restaurant bought options.  Here are the first 5 (click to enlarge):

Note the range!  How do I know whether my little homemade chef salad is more like Arby’s or Blimpie’s (which is FOUR TIMES as many calories?!?).     Also, we all know that the fat and calories in a salad is drastically affected by the type and amount of dressing – so do I really have to measure that out to the teaspoon to get a good measure?  Doesnt that take all of the fun out of eating?

I think I am going to struggle with this.   So far, the winner in terms of apps is the Livestrong MyPlate app.  It seems to me to have the most extensive database (e.g. it was the only one of the three that had an entry for ‘saag’), it is super easy to use, and has iPhone and iPad apps that all sync up effortlessly.   I’m trying to keep up with the logging, but finding it kind of a drag.  Even after just a few days it feels like a chore.  Anyone else out there have continued success with logging caloric data?

The other side is measuring how many calories you burn.  All of the apps have a database of activities you can choose from – everything from boxing to bowling to billiards to broomball – with estimated calories burned per time unit.  Even sexual activity is listed – which can be light, moderate or vigorous – in case you didn’t know.  For now,I’m settling for a combo of the Fitbit record of my steps and activity level, paired with Runkeeper logs of my jogging/cycling, and the Fitlinxx machine that is used at my YMCA.     What a mess! As this process goes on I’m certainly going to want to consolidate the number of apps/websites I use.

Older Entries Newer Entries