What I’m Reading: August 2018

Well it’s summer and we’ve had one heck of a heat wave up here, with humidity that I heard dubbed “sweatpants heat”. It’s gross. I’m particularly miserable about the whole thing because I’ve caught a terrible cold, which does not play well with the heat/humidity. I was thinking about the unique pain that summer colds bring, and decided to Google around to see if there was any research on this. Turns out there is! It appears that summer colds are actually caused by different viruses than winter colds, so the feeling that they’re a little different is a real one.

In other important news, this website went through and used the water displacement method to figure out the air to chip ratio for most common brands of chips. The results are oddly fascinating:

The Assistant Village Idiot did an interesting post about media bias, in the form of compiling Time and Newsweek covers of Presidents from Ford on. A quick look gives you a feel of how each President was portrayed. I previously might have argued that magazine covers didn’t effect me that much, but ever since I found out that I thought Billy Graham died years before he did (probably) because of a TV Guide cover I’ve been less confident about this. Donna B raises a good question in the comments about the covers given to those who ran for the presidency but lost during those years.

Some surprisingly bad news: a huge randomized control trial of state sponsored pre-K shows the positive effect is only present at the end of the pre-K year, and turns negative by 3rd grade with kids who went to free pre-K performing worse in math and science than their peers who stayed home. This is surprising as I thought the worst case scenario would be “no effect”. The study authors have two theories for the results. First, it’s possible some kids just do better at home. Second and not unrelated, they note that more of the kids in the pre-K program ended up in special needs classes (remember, they were randomly assigned to pre-K vs home) and they wonder if some slower to develop kids got inappropriately tagged as special needs. It appears this early designation then followed them and they may have eventually held back beyond what was needed. Still a good data point in the “not everything that sounds like a good idea is one” train of thought.

I’ve been thinking a lot about viruses and other various pathogens recently, and the theories that they impact chronic disease more than we realize at the moment. For example, a recent Harvard study suggests that the herpes virus may help precipitate Alzheimer’s Disease. Celiac disease may be triggered by a candida infection. Some strains of intestinal bacteria may make it really hard for people to lose weight. The mechanisms for this are interesting and varied. The Alzheimer’s theory hinges on the idea that amyloid-B (the thing that ends up clogging up the neurons in Alzheimers patients) is produced to try to fight off HHV-6 and HSV-1, but something gets out of control and it takes over. Candida and gluten apparently bind to the same site on the walls of the intestines, so the theory is the body starts trying to fight off candida but produces antibodies to everything binding at that site. Gut bacteria that thrives on sugar or other “bad” treats might release toxins when you stop eating it that make you feel miserable until you resume previous eating patterns.  One statement I read somewhere while reading this stuff stuck with me “maybe our pathogens didn’t go away when we invented antibiotics and vaccines, maybe they just got less deadly and more subtle”. I’m completely fascinated by these theories, though we’ll see if they pan out.


The Carlisle Method: One Year Later

Every once in a while the traffic on an old post goes through the roof, and I realize something interesting must have happened. This week it was my Carlisle Method post, which I appreciated because I had been meaning to check back in on that whole situation.

For those of you who didn’t read the initial post, here’s the overview:
An anesthesiologist came up with a neat statistical way of checking for data fraud. Rather than focus on the flashy results and conclusions of papers, he focused on the characteristics of the test group vs control group and looked for evidence that they weren’t random. The theory is that people committing fraud would mostly focus on their conclusions, but might get sloppy when reporting things like subject age and such.  He publicly named the papers he thought were most questionable, and investigations were launched.

A year later, some of the results are in. The New England Journal of Medicine announced their results, and they actually are a bit encouraging. Out of the 11 papers they analyzed, 5 had mislabeled “standard error” as “standard deviation” so the Carlisle Method was picking up on the error. 5 papers were reviewed and found to be okay, and they suspect some limitations in the Carlisle Method itself had wrongly flagged them.

One paper however, is getting lots of attention. It turns out that a major paper on heart health and the Mediterranean Diet wasn’t quite done as reported. While it had been reported as a randomized trial, a bit of digging showed that about 20% of its participants  were actually “cluster randomized”.  The authors reanalyzed the data using the remaining 80% of people, and noted that this didn’t change the conclusions, but it did make them less statistically compelling. The paper was retracted and replaced with a new version that correctly covers the methods.

Now all of these errors may appear to be small, but they do raise a bit of a cause for concern. There is an assumption that all statistics will be checked thoroughly before papers go to press, but I think this highlights that sometimes errors get through. Particularly if a paper has a big splashy finding, it’s possible that errors will not be reviewed. The NEJM shared this concern, and is implementing a statistics course for their editors and giving extra scrutiny to published papers.

More concerning than the NEJM’s findings however, is that the other 7 journals who had papers on the list haven’t completed their investigations yet, said there were no problems with any of the papers, or didn’t respond. It seems a little unlikely that only the most prestigious journal involved had any errors, so it’s unfortunate the other journals aren’t doing more.

More on the varied reactions to the Mediterranean diet study here and here.

Vitamin D Deficiency: A Supplement Story

I think I mentioned a little while back that I hadn’t been feeling so great and was going to slow my posting down for a bit. A decent amount of that “not feeling great” thing was related to a rather alarming Vitamin D deficiency I had unfortunately developed, and have since been treated for. This involved taking prescription strength megadoses, which helped almost instantaneously. It was lovely. As my doctor said “this is the best possible outcome. You came in with all sorts of symptoms and one simple thing fixed it.” I fully agreed.

It was an interesting thing to have happen because a few years ago another family member of mine had asked their doctor for a Vitamin D test and gotten an eye roll and a “that’s not really a thing we do any more”. Googling a bit, it seemed like there were nearly as many articles talking about how you shouldn’t take Vitamin D as those advising that you should. In classic “vitamins as fads” fashion, I noted that most of the pro-Vitamin D articles were from around 2010, and the anti-ones were much more recent. Combining my own experience with that of Dr Google, it got me thinking about how trends in supplements (or other medications or health behaviors for that matter) get going and why people then turn on them.

Step 1: Something that is under-recognized makes people feel terrible.

According to the American Association of Family Physicians, Vitamin D deficiency can result in “Common manifestations of vitamin D deficiency are symmetric low back pain, proximal muscle weakness, muscle aches, and throbbing bone pain elicited with pressure over the sternum or tibia.” Me? I had all of those symptoms. It sucked. I couldn’t sleep. Doing any activity left me sore and tired.

Now since Vitamin D deficiency is pretty well known, my doctor tested for it right away along with several other things. However, if it was not a well recognized deficiency and she had to fumble around a bit before she got there, I could have been living like that for months or years.

Step 2: People who feel terrible feel better, and are excited about their miracle cure.

Now I am pretty darn excited about my turn around on Vitamin D, as I think anyone would be. Again though, Vitamin D is a pretty well known deficiency, and lots of people I talk to have had the same experience or know someone who has. Thus, my compulsion to “evangelize” this solution is limited. A bad thing happened, the medical establishment addressed it immediately, and I am a happy camper. No real story there.

However, if I’d been feeling that way for months and my doctor had overlooked it, I’d want EVERYONE to know what happened to prevent the suffering of others.

Step 3: People who hear about this start to wonder if it’s their issue too.

Lots of people feel fatigued, or have aches and pains. The number who might hear my story and wonder if this Vitamin D deficiency were causing their might be much wider than the circle who would go in to their doctors and complain of the same thing. This isn’t bad, but it does mean that some of those people are going to have much milder symptoms than the ones I experienced, and those could be something else.

For example, what finally drove me to my doctor was being in so much discomfort that I was barely sleeping at night. I walk to and from the train every day (about 1.5 miles each way), and for a variety of reasons (including a weekend) I skipped about 4 days. When I started walking again, I was so sore I could barely stand when I got home. I felt like I’d run a marathon. That’s when I realized something was SERIOUSLY not okay. I’d been ignoring aches and pains for a few months, but you can’t ignore that.

So my issue got so severe I had to pay attention, but those who I tell about it are sort of having the information solicited. Two different groups.

Step 4: Some people figure if some is good than more is better.

There’s a lot of debate over what an optimal Vitamin D level is, but it will not surprise you to know that I was not in the grey area. I found this chart (unfortunately no source) that shows some of the controversy:

For reference, my level was 12. No one appears to debate that I needed treatment.

The controversy has arisen over some of those in between groups, like those in the 20-40 range. Some people say that they need more, but if they lack clear symptoms and hover around 35, is that really true?

To take it a step further, some people with aches and pains just start taking Vitamin D assuming that they are deficient with no testing at all. This is where things start to go off the rails a bit.

Step 5: The backlash

Okay, so now we’ve got people on supplements for levels that may or may not be dangerous, and bottles flying off the shelves at stores to treat people who may not have a deficiency. That’s when some people start to say “okay, pump the brakes here”.

What was a miracle cure for people with clear symptoms and a definitive deficiency now moves to something of questionable benefit for many many others. That’s when you get doctors who start eyerolling at things, rightly or wrongly.

Now all of this isn’t to say that I object to supplements, or people trying to find things that work. I don’t. That’s a good thing.  However, for whatever reason, we do seem to forget that many supplements or medications are only miracles when someone is really not doing well. If you look at the controversy over statins for example, it’s clear that much of it got stirred up when doctors started prescribing them to people with very few risk factors. The evidence that they work for those with high risk of heart attacks or stroke are pretty good, the evidence that they work for people with low risk is not great. I think we all want to believe that something that can take someone at high risk/severe pain back to normal will help those with mild risk/mild pain get back their too, but it doesn’t always happen that way.

I think this comes back to our weird tendency to assume all relationships are linear. Just another reminder that you can’t assume that. Now excuse me, I’m going to get a bit of sun.

Bilingualism in Units of Measure

Well, I’m back from Germany and everything went quite well, except for one little incident with a spontaneous bloody nose brought on by the descent in to the Atlanta airport. Thankfully there’s a bathroom before you actually have to go through customs in Atlanta (there was not in Stuttgart), because I’m pretty sure the border patrol folks would have been less than impressed at my attempts to clean myself up with my leftover bottled water and that weird mesh they cover the complimentary pillow with. Good times.

It was a fun trip overall, and my lack of German didn’t end up making a difference. The town we were in was a college town, so nearly everyone spoke English as a second language. It was a little interesting though, as it was clear very few people we talked to were used to conversing with native English speakers (we saw quite a few people conversing in English where it was clear they were both ESL with different primary languages), which led to some fascinatingly idiosyncratic translation issues. For example, one of the people we spent the most time with clearly only knew the pronoun “he” and applied it to everything. The sign above the coat rack in our hotel informed us “We are not responsible for your wardrobe”, which didn’t quite come off as I believe they intended it. Not judging of course, since it’s all better than my forays in to other languages, but I actually love seeing where the unusual phrasing comes up.

Anyway, while thinking about various translation issues, I started thinking a little bit about units of measure. There were a few times over the course of the week where distances or volumes came up, and I was interested to see that I have minimal problems translating kilometers to miles/pounds to kilograms/liters to quarts or vice versa. Part of this is just general quick mental math, but I did realize that I’m actually pretty comfortable in thinking in either the metric system or the US/imperial system. My engineering degree and lab work both used a lot of metric system units, and being a runner keeps you familiar with 5k and 10k distances, which make all the distance translations pretty straightforward.

The only unit I have real trouble with is temperature. I simply cannot think in Celsius. Every time I see a temperature in Celsius I have to spend quite a bit of time calculating before I get to the right ballpark. I’m not sure why this is, though I suspect it’s something about the simultaneous change in the magnitude of a degree and the reference numbers. Somehow trying to doing both at once throws me off.

I’m curious how many people are actually comfortable in both sets of units. I’m guessing there’s a strong influence of profession here.

On a related note, here’s the history of the US relationship to the metric system as told by NIST.

On an unrelated note, here’s a map of Europe and what each region calls Germany:

Apparently this is directly correlated with which occupants of Germany invaded which country first, though I can’t confirm that.

Weird Weather on Patriots’ Day

Well folks, tomorrow is Patriots’ Day/Marathon Monday here in Massachusetts, which means the kind of lousy weather we’re having is going to affect the Boston Marathon runners. That’s a pity, but I’m pleased that the weather was at least okay yesterday, as my son went to his first major league game with his dad and grandfather. Since he’s being raised in a mixed household (I’m a Red Sox fan as is his grandfather, his father is an Orioles fan), he went with an Orioles shirt/Red Sox hat outfit that apparently was quite a hit with the crowd. My husband was good natured about it, until he got stopped by the MASN camera crew who were wandering around trying to find a few Orioles fans in Fenway. He refused to risk being on an Orioles broadcast with a child in a Red Sox hat, so he pulled his spare Orioles hat out of his coat pocket and our kiddo got his TV debut. We haven’t been able to find the clip, but we’re still looking.

Anyway, with the weather going downhill today, my Dad and I started musing about the worst marathon weather we could remember. I mentioned 2012 when it got so hot that they proactively offered to defer entries, and my Dad mentioned that in 1976 it hit 96 degrees. This led me to a page on the Boston Athletic Association’s website about all the weird weather they’ve gone through over the years.

A few highlights:

  • 5 different years saw snow fall on the marathon
  • 1939 saw a partial eclipse
  • 3 years have seen driving rain
  • 1927 saw heat (84 degrees) and a newly paved road that melted under their feet
  • At least 4 marathons have been run in 90+ degree weather

I’m hoping that our weird weather gives hometown girl Shalene Flanagan an edge, as I’m cheering hard for her. The last time someone from Massachusetts won the Boston Marathon was Alberto Salazar in 1982, I think we’re due.

One interesting tidbit I never knew about Patriots’ Day: in Maine, it’s legally “Patriot’s Day”, which makes me incredibly happy. That is going to be my go to excuse if I screw it up at any point going forward.


Biology/Definitions Throwback: 1946

It’s maple syrup season up here in New England, which means I spent most of yesterday in my brother’s sugar shack watching sap boil and teaching my son things like how to carry logs, stack wood, and sample the syrup. Maple syrup making is a fun process, mostly because there’s enough to do to make it interesting, but not so much to do that you can’t be social while doing it.

During the course of the day, my brother mentioned that he had found an old stack of my grandfather’s textbooks, published in the 1940s:

Since he’s a biology teacher, he was particularly interested in that last one. When he realized there was a chapter on “heredity and eugenics” he of course had to start there. There were a few interesting highlights of this section. For example, like most people in 1946, the authors were pretty convinced that proteins were responsible for heredity. This wasn’t overly odd, since even the guy who discovered DNA thought proteins were the real workhorses of inheritance. Still, it was interesting to read such a wrong explanation for something we’ve been taught our whole lives.

Another interesting part was where they reminded readers that despite the focus on the father’s role in heredity, that there was scientific consensus that children also inherited traits from their mother. Thanks for the reassurance.

Then there was their descriptions of mental illness. It was interesting that some disorders (manic depressive, schizophrenia) were clearly being recognized and diagnosed in a way that was at least recognizable today, while others were not mentioned at all (autism). Then there were entire categories we’ve done away with, such as feeblemindedness, along with the “technical” definitions for terms like idiot and moron:

I have no idea how commonly those were used in real life, but it was an odd paragraph to read.

Of course this is the sort of thing that tends to make me reflective. What are we convinced of now that will look sloppy and crude in the year 2088?

I’m Thinking of a Word That Starts With a…..

I’ve mentioned before that I like to try to find unusual ways of teaching my 5 year old son statistical concepts by relating them to things he likes. This pretty much doesn’t work, but this week I tried it again and attempted to use a discussion about letters to segue in to a discussion about perception vs data. He’s getting in to some reading fundamentals now, and is incredibly curious about what words start with which letters. This leads to our new favorite game “Let’s talk about ____ words!” where we name a letter and then just think of as many words as we can that start with that letter.

This game is fun, but he’s a little annoyed at letters that make more than one sound. This week he got particularly irritated at the letter “c”, which he felt was hogging all the words while leaving “k” and “s” with none. I started trying to explain to him that “s” in particular was doing pretty alright for itself, but after discussing “cereal” and “circus” he was pretty convinced that “s” was in trouble.

As I was defending the English language’s treatment of the letter “s”, I started to wonder what the most common first letter of words actually was. I also wondered if it was different for “kids words” vs “all words”. After some poking around on the internet, I discovered that there’s a decent amount of variation depending on what word list you go with. I decided to take a look at three lists:

  1. All unique words appearing more than 100,000 times in all books on Google ngrams (Note: I had to go to the original file here. The list they provide on that site and the Wiki page is actually the most common first letters for all words used, not just unique words. That’s why “t” is the most common….it’s counting every instance of “the” separately)
  2. The 1,000 most commonly used English language words (of Up-Goer 5 fame)
  3. The Dolch sight words list, used to teach kids to read

Comparing the percent of words starting with each letter on each list got me this graph:

As I suspected, “s” does quite well for itself across the board, though it really shines in the “core words” list. “K” on the other hand is definitely being left out. It’s interesting to see what letters do well in bigger word sets (like c, p and m), and which ones are only in the smaller sets (b, t, o and w). “W” seems very popular for early reading lists because of words like “what”, “where”, “why”. “S” actually is really interesting, as it appears to kick off lots of common-but-not-basic words. My guess is this is because of its participation in letter combinations like “sh” and “sch”.

Anyway, my son didn’t really seem to grasp the “the plural of anecdote is not data” lesson, so I pointed out to him that both “Spiderman” and “superhero” started with “S”. At that point he agreed that yes, lots of words started with “s” and went back to feeling bad for “K”. At least that we can agree upon.

Now please enjoy my favorite Sesame Street alphabet song ever: ABCs of the Swamp