Someone wasted their time in biostats class

There have been many times when I’m standing before master of public health (MPH) students, giving them a presentation on epidemiology, and I wonder how any of them can even put on their shoes in the morning. Don’t get me wrong; they’re bright students. Many of them have graduated from college with impressive grades and great projects. They wouldn’t be in these top-notch universities if they were not bright. (Or if their benefactors didn’t see brightness in them.) Still, I’m not surprised when I see many of those kids getting an MPH in epidemiology and not become epidemiologist.

Being an epidemiologist is tough. It requires you to be able to think critically and analyze a problem from different sides and different points of view. Most public health problems requiring epidemiological analysis are big, huge puzzles with many working parts. Just being book smart is not enough. Being street smart is not enough. Being charismatic is not enough. Having an MPH in epidemiology or otherwise is not enough.

Like many people, I have issues completely comprehending biostatistical analyses. Biostats is tough. Few people get through it and continue to take classes in it. In fact, I look at the biostats crew at my job and shake my head in amazement. They can slice and dice data in ways I can’t even dream of. So I go to them with questions about biostats. It was one of them, a PhD-level young lady, who explained to me why the paper by Dr. BS Hooker was full of, well, BS.

I have never claimed to be all-knowledgeable on things like epidemiology and biostats. I just know what I know, and I know when to ask for help. I don’t like to pound my chest and say that I’m the best epidemiologist out there. I’m not.

So who wasted their time in a biostats class? Who else, the kid. What leads me to that opinion? First, some background.

In epidemiological studies, there is a hierarchy of what studies contribute the most evidence. At the very bottom is professional opinion. Surely, you would not guide public health policy based on what I or any other person would write on their blog or in an op-ed, or in a letter to the editor. Right above professional opinion are cross-sectional studies. Cross-sectional studies are basically surveys. You survey the population to get an idea as to what is going on before you move on to bigger, better-designed studies, like case-control and cohort studies. After case-control and cohort studies come randomized trials, where issues of confounding and bias are better addressed, and the results have a lot more weight on how to go about solving a public health problem. At the very top of the hierarchy are meta analyses and systematic reviews, where you take all the data from different studies and weigh all the evidence to separate the wheat from the chaff.

Did you notice how I bolded where cross-sectional studies lie on the hierarchy? Why would I do that? Again, some more background.

The paper by BS Hooker took the data from the DeStefano study and treated those data as a cohort study. That right there was one of many flaws in the BS Hooker paper. You don’t take case-control data (which was how the DeStefano study was conducted) and treat it as cohort data. You just don’t.

When the kid tried to defend the findings of the BS Hooker paper as if his life depended on it, using only a screenshot from a video published by Andrew Jeremy Wakefield (and nothing more), someone pointed out to him (again) the flaws in the BS Hooker approach:

“Hooker didn’t crunch the data as a case-control; he crunched it as a cohort study and without knowing temporality of MMR vaccination with ASD diagnosis, it’s dead in the water.”

The kid took exception to this and made what I believe to be the epidemiological and biostatistical mistake of the year:

“No, he crunched it as cross-sectional.”

I spat my coffee all over my desk when I read this. Not only did BS Hooker torture data, his protege is now saying that BS Hooker downgraded the way he treated the data. Remember where cross-sectional studies rank in the hierarchy? I mean, holy sh!t. I knew the kid wasn’t that good at epidemiology, but this confirms how bad he is with biostats.

The same commenter tried to correct the kid (again):

“Anyone looking at how he modelled the data can see that it was a cohort design and if that wasn’t enough, Hooker explicitely states that, “In this paper, we present the results of a cohort study using the same data from the Destefano et al. [14] analysis.” Taking a tumble down the hierarchy of study-design strength, particularly when the dataset available to him was sufficient to conduct a case-control is a bizarre strategy to salvage Hooker’s miscalculated results.”

But the kid can’t be wrong, not even in this case:

“He should have said cross-sectional in that sentence, but it doesn’t change the validity of his results. Relative risk would be more meaningful to the average person than odds ratios and this is an issue which effects (sic) everybody, so I would imagine that is why Brian Hooker conducted it that way.”

HOLY SH!T. He thinks that cross-sectional analyses are better than cohort, and better than case-control as well!!! Even worse, he thinks people are effected, not affected. So call the grammar police!

Of course, to the uninitiated, this doesn’t matter. To the true believer antivaxxer, the kid is an authority on epidemiology and biostatistics. God help anyone who places their faith on him for analysis of scientific evidence. But thank God that, although my comments are not being allowed through by the kid, he allows comments from other people who can see through his, well, BS.

If you have some minutes to waste, and you want to have a good laugh, go read the comments section of the kid’s blog post. It’s comedy gold. If you know epidemiology and biostatistics, you’ll have a good laugh at the errors in logic and reasoning that are pervasive throughout his commentary and his readers’ comments.

This was the eighth post that has nothing to do with vaccines, for the most part.

Just in case there was any doubt

Ren wrote a great post on his blog the other day on what makes an epidemiologist. He didn’t mention The Kid (a.k.a. Jake Crosby) by name, but I’m pretty sure that’s who Ren was talking about. It seems that Jake Crosby, on account of having earned a Master of Public Health degree from the George Washington University, fancies himself an epidemiologist. I agree with Ren that people like Jake Crosby are not and never will be epidemiologists. Jake Crosby is not an epidemiologist because he does not work as one — to the best of my knowledge — and, most importantly, he is not an epidemiologist because he believes that vaccines should be eliminated altogether. Anyone with an ounce of decency and common sense in their bodies would not call for the end of something that has saved countless lives.

Just in case there was any doubt of his stance on vaccines, on his blog, this is what Jake Crosby wrote when one of his readers suggested that we (humanity) vaccinate no more:

The book in question is a new book by RFK Jr. about vaccines and neurodevelopmental disorders. As you can see, Jake Crosby and his reader appear to have developed a macropapular rash when the book is quoted as lauding vaccines for the “achievement in medical science” that they are. “That ingredient” is thimerosal, a compound that contains mercury but is touted as being nothing but mercury by people like Jake Crosby and others. Jake Crosby is apparently angry because one of his (apparently former) idols, Robert Kennedy Jr., is promoting a book about thimerosal causing, among other things, autism but doesn’t go as far as to call for the end of vaccines.

There was a time, way back when, when I would have given Jake Crosby the benefit of the doubt and chalked his anti-vaccine screeds to him just being fed anti-vaccine lies by his friends at Age of Autism. Today, Jake Crosby is an adult who has attended a four-year college and a two-year master’s degree, has been given all the tools of epidemiology to use, has been given all the evidence when it comes to vaccines, and he still calls for the elimination of the vaccine program. How he can classify himself as an epidemiologist after writing those things is beyond me, and beyond reason.

I think Ren went lightly on Jake Crosby’s antics. Me? Not so much. Jake Crosby will never be an epidemiologist because epidemiologists read the evidence and come to the reasonable and proper conclusions. They don’t see monsters under the bed or chase windmills. They don’t call for the elimination of the vaccine program and thus, in essence, call for the return of diseases that would kill thousands upon thousands of children worldwide every day. It’s par for the course for anti-vaccine types, however.

Spitting on the graves of children lost to influenza

A friend of mine who has worked in influenza surveillance for years send to me this blog post from the Huffington Post. It’s written by Lawrence Solomon, who, by all accounts, has zero experience in infectious diseases or epidemiology. Still, that doesn’t stop him from attempting to write about influenza deaths in an authoritative way, quoting, what else,  anti-vaccine and anti-science material. In fact, I need not go farther than his first sentence to know what he’s all about in this post:

“Flu results in “about 250,000 to 500,000 yearly deaths” worldwide, Wikipedia tells us. “The typical estimate is 36,000 [deaths] a year in the United States,” reports NBC, citing the Centers for Disease Control. “Somewhere between 4,000 and 8,000 Canadians a year die of influenza and its related complications, according to the Public Health Agency of Canada,” the Globe and Mail says, adding that “Those numbers are controversial because they are estimates.””

Why are these number estimates? It’s simple. We can’t possibly count each and every single case of influenza, or influenza-related deaths, in the world. What we can do is use the tools of science and mathematics to come up with a best estimate. If you read further in Lawrence Solomon’s piece in the Huffington Post, you’d think that we epidemiologists come up with these numbers at random, or, if we do use science and math, that we adjust those numbers to some sort of agenda. To make his point, Lawrence Solomon goes to the latest go-to guy in Peter Doshi, PhD (who is not an epidemiologist of any sort but still wants to be some sort of authority on influenza and influenza vaccine science):

“Peer reviewed publications accept Dr. Doshi’s vaccine research, even if he doesn’t meet your standards. But are you saying that you would accept the views of epidemiologists who turned thumbs down on vaccines? It would be my pleasure to present some to you, if that is your test.”

Influenza is here, it’s bad, and it’s killing people

Contrary to the opinions of people like Peter Doshi, PhD, and others that influenza is not that bad, influenza is pretty bad. Just ask the family of this woman in Texas how bad it is. Or ask the family of this girl. Influenza is being reported from all over the lower 48, Canada, and Mexico. Many public health agencies are now recommending the influenza vaccine as a countermeasure to the increase in cases. As an epidemiologist, I join other epidemiologists in saying that the vaccine is not a good countermeasure, and it shouldn’t be used as the lone countermeasure. It takes a while for it to confer immunity, so it may be too late now that the season is fully underway.

So-called epidemiologist doesn’t understand epidemiology

The kid wrote this:

“Regarding the data you speak of, I cannot publish it because I do not have access to it nor is it in my possession. We know [autism] is declining because it was discussed in email by a coauthor of then-principal investigator/now-most-wanted fugitive Poul Thorsen’s thimerosal study in email to Thorsen, his then-student and first study author Kreesten Madsen and CDC employee Diana Schendel. A much later study coauthored by Schendel was just recently published showing ASDs going down in years following thimerosal’s removal from Danish vaccines:”

He then links to this study from the University of Miami. From what he wrote above, you would expect that the paper addressed or studied a decline in the number and proportion of cases of autism in Denmark after thimerosal was removed from childhood immunizations. Did the paper address or study this?

Reading For Comprehension

Humor me and read the following abstract of a study:

“Background The GARDASIL long-term follow-up (LTFU) study is an ongoing extension of a pivotal randomised, placebo-controlled, double-blind, 4-year study to investigate the safety, immunogenicity, and effectiveness of quadrivalent Human Papillomavirus vaccine (qHPV) on the incidence of HPV 16/18-related cervical intraepithelial neoplasia (CIN) 2 or worse in 16–23-year-old women (Protocol 015).

Methods Follow-up of subjects will be accomplished in two ways: (1) registry-based follow-up for effectiveness data as well as safety data including but not limited to deaths, cancer, and hospitalisations; (2) active follow-up for blood collection for immunogenicity assessments at years 5 and 10 of the LTFU study. Effectiveness and safety analyses will occur approximately 2 years following completion of Protocol 015 and approximately every 2 years thereafter for 10 years. The current report represents the first of these efficacy and safety analyses. Cohort 1 included approximately 2700 subjects who received qHPV vaccine at the start of Protocol 015. Cohort 2 consists of approximately 2100 subjects who received placebo at the start of Protocol 015 and qHPV vaccine prior to entry into the LTFU. Vaccine effectiveness against HPV 16/18-related CIN 2 or worse was estimated by calculating the expected incidence of CIN 2/3 or worse in an unvaccinated (placebo) cohort using historical registry data. The primary analysis approach was per-protocol.

Results There were 1080 subjects that contributed to the follow-up period out of a total of 2195 eligible subjects in the per-protocol population in Cohort 1. In these subjects there were no cases of HPV 16/18-related CIN 2 or worse observed. There were also no cases of HPV 6/11/16/18-related CIN, vulvar cancer, and vaginal cancer observed. However, the follow-up time in person-years is insufficient to make a definitive statement about the effectiveness of the qHPV vaccine for the current time period.

Conclusions The qHPV vaccine shows a trend of continued protection in women who were vaccinated up to 7 years previously, although there is as yet insufficient data to confirm that protection is maintained. The qHPV vaccine continues to be generally safe and well tolerated up to 6 years following vaccination.”

You can go ahead and re-read it if you didn’t quite catch something.

US girls decide to become less slutty, wash their hands, or get vaccinated? You tell me.

The NY Times is reporting a study published in the Journal of Infectious Diseases where it is reported that the prevalence of HPV infection in girls ages 14 to 19 is half of what it was in 2006. So what happened? Did these girls decide to be “less slutty“? Did hygiene and sanitation finally make their way to these girls’ vaginas? No.

What happened was that anti-HPV vaccines came online in 2006, and lots of girls are getting them. Lots, but not as many as we need to sustain this decrease. We’re far behind other countries in that respect. According to CDC:

“This report shows that HPV vaccine works well, and the report should be a wake-up call to our nation to protect the next generation by increasing HPV vaccination rates,” said CDC Director Tom Frieden, M.D., M.P.H.  “Unfortunately only one third of girls aged 13-17 have been fully vaccinated with HPV vaccine.  Countries such as Rwanda have vaccinated more than 80 percent of their teen girls. Our low vaccination rates represent 50,000 preventable tragedies – 50,000 girls alive today will develop cervical cancer over their lifetime that would have been prevented if we reach 80 percent vaccination rates.  For every year we delay in doing so, another 4,400 girls will develop cervical cancer in their lifetimes.”

Most of you will know that HPV vaccine continues to be demonized, against all the evidence, and anti-vaccine people keep blaming deaths and disabilities on it. A presidential candidate fueled the fire based on similar misconceptions about the vaccine. But, guess what? The evidence keeps coming in. The vaccine is safe, effective, and it is cutting infections in half. Now, we need to replicate these findings in those highly-vaccinated countries to put yet another nail in the coffin of the HPV vaccine conspiracy.

Mental exercises for a better brain

There’s this discussion going on over at Respectful Insolence between an anti-vaccine activist and an epidemiologist, like me. The anti-vaccine activist — whom I thought was banned from there (oops) — is known to be quite “dense” when it comes to epidemiology and biostatistics. I don’t blame him, much. His highest degree in science is in Fire Science. I don’t know where this guy when to school, but most programs I’ve found, like this one, don’t have biostatistics or statistical reasoning in their curricula. This would explain the activist’s misunderstanding of a case-control study. Like the PhD in Biochemistry being discussed by Orac in that post, the activist thinks that matching cases and controls in a study somehow disallows for the examination of their vaccine status and its relationship to autism. They think that cases (autistic children) should have a different vaccine status than controls (neurotypical children), and then we can see if they have a difference in vaccine exposures.

Can you see the logical fallacy in that?

Autism: It is not a disaster

Believe it or not, people who are mentally ill are more likely to be victims of violence than perpetrators of violence. This doesn’t make much sense to people because we want to believe that someone who kidnaps, rapes, and murders a person has to be deranged. A “normal” mind can’t possibly do something so horrible, right?

Even worse, a lot of people are quick to point out that a criminal — especially a young criminal — was kind of “quirky” or maybe had “autism or something” instead of waiting for the facts to come through on a case. I believe that it’s our own attempt to justify what happened and to tell ourselves that we would never do something like that. Because, deep down, we’re afraid to be monsters ourselves.

Don’t deny it. It’s true.

Furthermore, autism and other neurological disorders are not mental health problems. You wouldn’t walk up to someone with cerebral palsy and say that they’re “crazy,” would you? Likewise, you wouldn’t say that Muhammad Ali, who has Parkinson’s, is more likely to commit violence than someone who is neurotypical. Would you? Nevertheless, for a very long time, children with cerebral palsy or autism have been treated as being “crazy” or “quirky,” and mass shooters as possibly being autistic (with the implication that said autism was the cause for their violence).

And so we come to yesterday’s news that “1 in 50 children have autism.” From Dr. Willingham’s post:

“According to the CDC, hidden within these numbers is the finding that most of the increase from 2007 to now occurred in school-aged children. In other words, given that it’s possible to diagnose autism as early as age 18 months and usually by age 5, many of these new autism diagnoses were in children who received them relatively later. Children who were, therefore, walking around for quite a few years with autism that went unrecognized … and uncounted. That fits with the idea that a lot of the increase in autism we’ve seen in the last decade has much to do with greater awareness and identification.”

The anti-vaccine blogs are already chomping at the bits at what this new prevalence number means, totally misunderstanding the meaning of the data. (I’m not surprised, are you?) Not only that, but they have their dire predictions:

“Any expressions of concern from anybody with the power to do something about this disaster? No . And the press, as usual is soft pedaling the findings. Fifteen years ago the autism rate was 1 in 10,000, 12 year ago it was I in 2,500, 10 years ago it was 1 in 1000, and so on. When President Obama was elected in 2008 the official rate was 1 in 150, then it went to 1 in 88 and now it is 1 in 50. Where is it going to stop?”

It will never stop. We will get to 100% saturation. Every child will be autistic.

I’m joking, of course. The prevalence rate will remain the same as it has always been. Our estimate of it will even itself out and approach the prevalence rate and remain there. This is because our ability to do surveillance for autism is improving. The identification of cases by healthcare providers is improving. People with autism are coming forward and demanding to be counted. Our elected leaders are devoting more resources to ways to assist people with autism to lead long and productive lives. These are all good things.

It is not a disaster.

What is a disaster is that people who call themselves “advocates” for children and adults with autism continue to say and do things that actually harm people with autism and other neurological disorders. They call it a “disaster” to have a child with autism, or they say that they “lost” their child to autism. They then write that their children are monsters or have monsters inside them. And we’re supposed to just stand back and be understanding because we don’t have children or children who are autistic? We’re supposed to agree that it’s a “disaster” when all rationality says that it’s not and that children with autism can and will grow up to be productive citizens who even appear on CSPAN as advocates of people with similar neurological disabilities?

No, we’re not. I won’t. And I hope you won’t either.

Vax vs. Unvax studies… FIGHT!

This doctor is asking that we do a vaccinated vs. unvaccinated study to determine if vaccines cause more or less “outcomes” (read: autism) than what is attributed to them. I never went to medical school, but I did go to epidemiology school with a lot of medical students. Maybe this doctor was too busy with other things when he was introduced to epidemiology, because it is very clear that he has no clue what he is asking for. (Or maybe he is just selectively remembering what is good for him and what isn’t?) See, in the world of epidemiology, there is a hierarchy of epidemiological studies. In ascending order of ability to show causality, the studies are these:

• Case Study (describing one person with the condition, a case)

• Case Series (series of cases)

• Ecological Study (analysis of group statistics..for example, comparing rates of disease between two countries)

• Cross-Sectional Study (assessing individuals at one time, such as a survey)

• Case-Control Study (studying those with the condition vs. those without)

• Cohort Study (following subjects over time to study the initiation and progression of a condition)

We did the case studies. We looked at children with autism and determined that there was no biologically plausible way for vaccines to cause autism. Furthermore, instances of unvaccinated children with autism kept coming up. There were even case studies of autism before many vaccines were around. So we moved one step up.

We did the case series. We looked at groups of children with autism and determined that some were vaccinated while others weren’t. Even within those who were vaccinated, we noticed that their symptoms preceded vaccination. In those who were unvaccinated, we noticed that their symptoms were similar to children with autism. And, like with the case studies, we found that vaccines have no biologically plausible way of causing autism. So we moved one step up.

We did an ecological study. We looked at autism rates in other countries and in this country. After adjusting for differences between factors in the different countries, we found that there is no difference between countries in the rates of autism. Furthermore, there are differences between those countries when it comes to vaccine availability. That is, it didn’t matter if the countries vaccinated more or less, we found no difference in autism rates. So we moved one step up.

We did surveys. (Heck, even the anti-vaxers wanted to do surveys.) And, after adjusting for all sorts of biases that surveys present, we found no difference between vaccinated and unvaccinated groups. (The anti-vaxers found a similar result, but that doesn’t stop them from wanting another round at it.) So we moved one step up.

We did case-control studies. We took children who had autism and children who had no autism, then we looked at their immunization records. It turned out that both groups had equal odds of being vaccinated. There was no difference between the two groups.

In short, everything we’ve done to date has failed to find a link between immunizations and autism. So you would think that the vaccine-autism link would be dead. Well, it isn’t. That doctor I told you about in the opening sentence wants a cohort study (aka Randomized Clinical Trial or Randomized Controlled Trial). Never mind the millions of dollars and thousands of man-hours lost doing such a study when all the previous evidence has shown no link. Never mind that we could do much better things with those resources. No. The anti-vaccine groups want to slay their dragon. They want to prove that vaccines did to them what they think vaccines did to them.

So what would it take to do such a study? Well, it would go like this:

Recruit participants at birth. Parents would be approached and told that their child would be participating in this study. Without their knowledge, their child would be assigned to one of two groups. One group is vaccinated while the other is given placebos. If you really want to give this study strength, you keep the group assignments secret from even the researchers.

Follow participants until a certain endpoint. This endpoint can be anything you want it to be: the diagnosis of autism, the age of ten — after which a diagnosis of autism is very rare, death, anything. Once all your participants reached the endpoint, then the study is done.

Analyze the data. You would then “unmask” the participants’ assignments and compare the vaccinated to the unvaccinated groups to see which of them reached those endpoints faster or in greater proportion. Which group has the most autistics?

However, can you see why this study is unethical and very likely to fail? First off, one half of the children — those assigned to the unvaccinated group — would be deliberately unprotected against some very nasty diseases. You tell me if you want your child to be unprotected against measles. If you’re an anti-vax parent, you probably don’t care. You probably think that your child will survive anything and come out stronger, despite all the evidence to the contrary. But what if you’re a pro-vaccine parent? Would you like your child to maybe not be vaccinated? And, if you’re anti-vaccine, would you like for your child to maybe be vaccinated?

Then there is the issue of bias. If you’re an anti-vaccine parent, and you think your child was vaccinated, you might make a bigger deal out of every little developmental delay. If your child doesn’t walk at 12 months, taking a few more weeks to get going, you might be more inclined to blame the vaccines. Or you might give your child an unproven therapy to try and “detox” them, and it might be that therapy that makes them ill.

On the other hand, if you’re a pro-vaccine parent, you might take your child to get a second round of vaccines if you think that your child ended up in the unvaccinated group. You want to make sure your child is protected, and, frankly, I can’t blame you for that. Also, being the responsible parent that you are, you might take your child to regular check-ups and discover autism (or any other “outcome”) much earlier than people who don’t take their children for check-ups.

And that’s just a few of the biases that could creep into this study.

The biggest problem with the study will be the deliberate lack of vaccination of half of the participants. No Institutional Review Board will allow you to do this because the liability is too great. If one kid in the control (unvaccinated) group get sick and dies from a vaccine-preventable disease, you will no longer be allowed to conduct research on human subjects, ever.

Of course, anti-vaccine activists will say that there are plenty of unvaccinated children, so finding children whose parents will deliberately leave them vulnerable to deadly pathogens wouldn’t be a problem. In that case, you’re not asking for a randomized clinical trial because you’re removing the “random” from it and you’re inserting a huge bias. If you see vaccines as an evil big enough to keep your children from being vaccinated, how likely are you to report that your child has autism, thus disproving your theory? In these cases, you’re asking for a case-control study, which has been done over and over again.

How much time, money, and God knows what other resources do you want us to keep on wasting in order to slay your dragon, to chase down your windmills, to find the bogeyman under your bed?

Then again, it’s not like ethics have kept the anti-vaccine forces from doing their thing.