The William Thompson Documents. There’s no whistle to blow.

4 Jan

For those unfamiliar with the story of William Thompson, here’s a brief introduction. William Thompson is a CDC researcher who has worked on vaccine/autism studies. About 2 years ago he approached Brian Hooker (an autism parent and very vocal advocate for the idea that vaccines cause autism) stating that a statistically significant result was not only left out of an old study but that this represented not a scientific decision, but misconduct on the part of the CDC. It is worth noting that “statistically significant” is not the same as “proof of a connection”. Brian Hooker published his own analysis (incorrectly claimed as being the same as the CDC analysis method) in a now retracted paper. The result he presented was that there was an apparent increased risk of autism for one small subset of the study population: African American males, who were vaccinated not on schedule but before age 3.

There are some questions, of course, that this raises. Is this result very strong? Does the lack of inclusion in the paper represent scientific fraud or a legitimate scientific decision?

A few epidemiologists and other scientists have chimed in (for example here, here and here) and stated that the result was very likely spurious and that Hooker’s approach is somewhat flawed and definitely overplayed.

In fact, Brian Hooker’s paper was more of a publicity event than a scientific inquiry. When the paper was published, Brian Hooker and Andrew Wakefield released a video. It is difficult to describe just how bad this video was but here are a two examples. Wakefield tried to put forth the inflammatory claim that the CDC’s vaccine program was a new Tuskegee experiment. Which is to say that the CDC are intentionally allowing African Americans to become autistic due to vaccines as part of some sort of study. Second, according to Andrew Wakefield, the CDC team is so evil that they are worse than Hitler, Pol Pot and Stalin. =Mr Wakefield’s logic being that those dictators were sincere and the CDC team were not. No, really, Hitler was sincere per Wakefield.

In a series of phone calls between Thompson and Hooker (secretly taped by Hooker and released without Thompson’s permission), we find that Thompson was very interested in testifying before congress. It turns out that William Thompson kept much (if not all) of the paperwork involved in this study and, probably at least in part motivated by the hope for a hearing, passed these along to a member of Congress: Bill Posey. It has been claimed that this cache of documents numbers as many as 100,000 pages. Many have hoped that these documents will expose fraud by the CDC. (They don’t)

Congressman Posey released the documents to a journalist recently and, given that they are now in the public domain, Dorit Reiss and I requested that they be made available to us as well. Mr. Posey’s office graciously granted our request and I have spent some time going through them.

For those hoping for an exciting look into CDC malfeasance, sorry to disappoint you. Not only is it not present here, but these documents are very mundane and repetitive. Many people seem to think there will be evidence that the CDC are covering up. No “Vaccines cause autism! How do we cover this up”. Nothing like it. Wakefield and Hooker have already cherry picked–and misrepresented–whatever they could to “best” make their case.

For more introduction, I point you to these articles as a start:

MMR, the CDC and Brian Hooker: A Guide for Parents and the Media

Did a high ranking whistleblower really reveal that the CDC covered up proof that vaccines cause autism in African-American boys?
The “CDC whistleblower saga”: Updates, backlash, and (I hope) a wrap-up
Brian Hooker and Andrew Wakefield accuse the CDC of scientific fraud. Irony meters everywhere explode.

Given that long introduction, what is in the documents? Well, there’s about 1000 pages, not the claimed 100,000. Documents provided by Mr. Thompson and, also, documents that submitted as part of the complaint that Wakefield and Hooker filed with HHS were included in the zip file. Which is convenient as I had submitted a FOIA request for those.

There are multiple drafts of the analysis plan. Analysis Plan is the same thing as the “protocol” that Wakefield and Hooker claim was changed after the first race data were analyzed. And the fact that we have the revisions gives us the chance to check two of the fundamental claims behind the Wakefield/Hooker “fraud” charge against CDC. (1) Did the CDC plan to look at race as an exposure variable? Wakefield and Hooker are claiming (although they use different words) this is what the CDC was doing. This is different from using race as a control variable. (2) Did CDC add the birth certificate analysis after the first race analysis was done, in order to dilute the effect?

No. Very clearly no. I’ve covered (2) already based on information Wakefield and Hooker made available. The final analysis plan was dated Sept.5, the first race analysis wasn’t until late October or early November. And we see the same in these documents.

But now we have new information that answers (1). Here is what appears to be the first draft of the analysis plan. And here is a capture of a very important part:

First Draft Analysis plan segment 1

Note that this draft analysis plan is from April 3, 2001. Well before the final version, the “protocol”, which was September 5. More importantly, this is a long time before a race analysis was started. But even more, notice how there’s an annotation “I would include race as a covariate, not as an exposure variable.” That’s critical–they decided against using race as an exposure variable from the start. Before they did a race analysis. Another point: they were already planning on using birth certificate data right from the start.

William Thompson certainly should have known this, it’s very probable that he did know this. Wakefield and Hooker likely knew this. They showed documents from this collection in their video and elsewhere. But they told us the opposite.

Whether they knew or not, they were wrong. Wildly irresponsibly wrong.

Ever wonder why they didn’t make documents public? We can’t tell if Hooker and Wakefield had all the Thompson documents, but we know they had some. While they cry out for transparency, they were carefully guarding information in order to craft the story they wanted told. The full documents tell a different story.

Let me put this more simply: if Wakefield and Hooker worked for me they would be fired for just their handling of the Thompson story (of course, they would have been fired years ago for many other causes, but promoting this sort of misinformation is simply wrong.)

Also in that same directory appears to be the first draft of the paper (A000071.PDF), with William Thompson as first author. I find it interesting that Thompson is first author there as later it would be Frank DeStefano who would be first author of the published study.

There are also meeting notes. Lots of meeting notes. Here’s the first batch, as near as I can tell. Meetings were held every month or two.

Now is a good time to address the “garbage can” quote. Congressman Posey read a statement from William Thompson into the congressional record. Emily Willingham discussed this in A Congressman, A CDC Whisteblower And An Autism Tempest In A Trashcan. On the other side, here’s an article by Jon Rappoport Bombshell: CDC destroyed vaccine documents, Congressman reveals Bombshell: CDC destroyed vaccine documents, Congressman reveals; CDC whistleblower case is back.

Here’s the thing–there’s zero “bombshell” involved in putting these documents into a confidential bin for shredding/recycling. There’s no reason to keep all these revisions of the analysis plan, all these meeting notes, all this redundant material. I hope people at CDC are not keeping all this paper. Beyond that, the rules are that they have to keep enough information to recreate the study. Aside from the fact that all these meeting notes are not required for that, Brian Hooker proved that requirement was met when he claimed to have done exactly that–recreated the study.

Mr. Thompson also provided a file with ALL Agendas for mmr autism meetings with written interpretation. Which is to say Thompson added his own annotations (purple pen) to the agendas.

Here’s an example of his annotations. And a great example of trying to make data fit a story. Thompson appears to be trying to support the idea that the CDC team changed the protocol to include the birth certificate analysis in response to analyzing the race data:

Race examined before final protocol

The implication that the race analysis and had somehow influenced the final protocol (as Wakefield and Hooker have claimed and this comment appears to support) is just plain wrong. First, as we have already seen, the birth certificate analysis was included from first draft of the analysis plan, in April 2001. That’s four months before this meeting note. Second, the so-called “race effect” isn’t seen in this meeting note. In fact, we see the opposite: “not statistically associated with case/control variable”.

From the phone conversations between Brian Hooker and William Thompson (secretly taped by Hooker), we have found that Thompson was very interested in participating in a congressional hearing. Hooker and his colleagues had been involved in arranging a previous congressional hearing on autism. Frankly it appears to me as though Thompson was involved in a bit of a quid pro quo: Thompson coaching Hooker in ways to spread fear about vaccines in exchange for a chance to be involved in a hearing. Which begs the question: why no hearing based on all that Thompson has laid out?

In case it isn’t already abundantly clear: there’s no hearing because there is no reason for a hearing. There’s no evidence of fraud. Many of the reasons given by Wakefield and Hooker to call this fraud are, well, just flat out wrong. Contradicted by the evidence. For those hoping that Thompson’s personal notes would show some evidence of a cover up, here they are mmr autism study 2001-2002 hand written notes.

Ah, one will say, what about the finding of an association between the MMR and autism for African American boys vaccinated late (between 18 months and 36 months)? Why wasn’t that included in the published paper or public presentations? The reasons given by Thompson/Hooker/Wakefield don’t hold water as I’ve shown. So, what was the scientific reason for not including this result in the paper? Many online writers have discussed how weak this result is; how it is a spurious result. But I’d like to know the reasoning at the time behind the CDC decision to leave this out. As a community member–an autism parent–I’d like to see all the results and understand the reasons why certain results are spurious. Of course it is easy to say now, but leaving this out of the public’s eye was a mistake. It gave Thompson, Hooker and Wakefield the chance to cherry pick, hide information and craft a story that has been very damaging to the autism communities and to public health.

The first thing I did when I heard about this story was email a few epidemiologists I know and point this story out and ask them if they had the data to address the question raised. I no longer feel this way. Why should the autism communities spend precious funds and researcher time every time Andrew Wakefield (Time Magazine’s #1 on their list of great science frauds) comes up with a new story? Especially now that we know the story was built on lies. But consider this: Wakefield and Hooker have not been calling for more research. Instead they are calling for a congressional hearing. If you watched any part of the previous hearings you know they are political theater and have done nothing (NOTHING) to help make a better life for autistics. They have done nothing except provide video and blog fodder for those promoting the failed idea that vaccines cause autism.

Also, consider this: before Thompson Wakefield and Hooker didn’t talk about the issues of racial/ethnic minorities. For the most part, the entire “autism is caused by vaccines” community have ignored minority communities. Why? Because they are a clear example that the vaccine hypothesis is a failure. Prevalence estimates for racial/ethnic minority groups have been typically much lower than for Caucasians (Hispanics are diagnosed at a rate of 1/3 that of Caucasians in California. And this has been consistent for over 10 years.) This presents a huge problem for the likes of Hooker and Wakefield. If vaccines are a major cause of autism, why do minority groups have such low prevalences? If they were honest about their own beliefs, they would be calling for a study into the “protective” effect for minorities. But they don’t. More importantly, if they were real autism advocates they would be calling for better diagnosis, better awareness, better services for these under served communities. Instead they have just ignored these minority communities. That is, until they could use them as part of their campaign against vaccines.

And they still aren’t calling for better services better diagnosis in these underserved groups. Instead they are just trying to recruit as many parents as they into the vaccines-cause-autism camp. Imagine being convinced, wrongly, that you participated in injuring your own child. The charlatans who prey on our community with fake–and sometimes abusive–therapies rely on the vaccine/autism idea for the majority of their business.

The vaccines-cause-autism story is built on lies and it is very damaging. There has been nothing since the Kanner/Bettleheim “refrigerator parent” idea that has caused so much damage to our community. And that is the real story here. A group of people perpetuating a failed idea by carefully crafting a story.

The Zip file provided to me by Representative Posey’s office is at this DropBox link

Again, I am grateful to Representative Posey and his staff for providing these files to me.

By Matt Carey


122 Responses to “The William Thompson Documents. There’s no whistle to blow.”

  1. Kenneth Wiezer February 16, 2017 at 17:47 #


    • Sullivan (Matt Carey) February 18, 2017 at 00:52 #

      Here’s the thing, most kids with and without ADD were diagnosed after their vaccines. Kids with ADD and no vaccines are diagnosed.

      Which is to say, you present no evidence that there is anything to link vaccines with ADD.

      That said, did you bother to read the article above? Your comment shows no evidence of that. Especially since it has nothing to do with the article.

      • zshilor March 3, 2017 at 14:13 #

        There is no reason to assume that the effect of vaccination would be only in one direction and therefore it is relevant to bring other effects to the table. Even if we don’t have a research proving it, we should assume that this is a case, until valid independent researches have been done, outside the big pharma, and CDC.
        The CDC opposed to a control experiment vs. unvaccinated population, which defies common sense.

      • Sullivan (Matt Carey) March 3, 2017 at 15:22 #

        Your comment defies common sense. As in it is common sense to be clear and accurate.

        We have research showing that the vaccines cause autism notion is false. It is valid research. Much of it independent.

        But it comes to a conclusion you apparently disagree with. Which for many will make it not “valid” as you put it.

        The CDC would do a vaccinated vs unvaccinated study. Get them the funding and directive.

        Or sit back and complain that they won’t do it–even though you already made it clear that no matter they do you will consider it invalid because it isn’t independent of themselves.

        Seriously, put together a logical self-consistent argument.

  2. Beta Thanyou March 16, 2017 at 11:17 #

    That’s Pretty basic and cherry picked straw man argument that failed to deliver.

    • IVAN March 31, 2017 at 02:15 #

      “The CDC would do a vaccinated vs unvaccinated study. Get them the funding and directive.”

      Did you just asked people to give THEIR MONEY to the CDC to do THEIR OBLIGATED job?

      Each and every fucking vaccine or medicament/pill/ let’s call them medicine, MUST be tested prior take it to public use, don’t you agree?

      They are making TRILLIONS, without doing the SIMPLE vaccinated vs. non vaccinated tests?


      I bet you DO test the quality of whatever drugs you take, before taking them, cuz obviously you do consume some serious, brain damaging shit dude.

      Shame on you, your scam website, and the sponsor who are keeping you alive to serve misleading data.

      Soon everyone involved in MMR falsification will face the true judge. No, not the one you hope you can buy off.

      • Sullivan (Matt Carey) March 31, 2017 at 18:19 #

        Wow, I bet you actually think that was a stinging rebuke. Given the all caps an all.

        Why should CDC do a very expensive study? Well, for one, if there is evidence that it is needed. With the idea that vaccines cause autism, they

        If you think that a vaccinated vs unvaccinated study is “SIMPLE”, you clearly have no idea of what you are talking about. Do it yourself. It’s simple, right? Why hasn’t a real vaccinated vs unvaccinated study been done by the creduluous researchers who claim vaccines cause autism? Because it’s not simple. It’s very difficult, very expensive. Do you know how many people would have to be involved? And what is needed to tease out the biases in the unvaccinated population?

        Wakefield and the Geiers, with help from unethical political pressure, got ahold of medical data from Florida years ago. YEARS ago. And still no vaccinated/unvaccinated study. But it’s easy, right?

        And you think the CDC should just drop everything and do this on the account of the junk science that’s been used to attack vaccines?

        Sorry dude. Come up with a real reason. Not an “I’M USING ALL CAPS ON THE INTERNET” argument. Facts.

        The CDC has spent tens of millions of dollars chasing down false claims about vaccines causing autism. Money and time that could have been used for something valuable. Largely because of fraudulent research propogated by failed mediocrities posing as researchers. So, spend many more millions on a study you will no doubt decry as being biased? That’s just not a good basis for spending tax dollars.

        Soon everyone involved in MMR falsification will face the true judge. No, not the one you hope you can buy off.

        Ah, the old “the truth will come out” and “you are just a pharma shill” arguments repackaged.

        The truth did come out. Vaccines don’t cause autism. And if there are people I can “buy off”, they are very cheap. By the way, you are supposed to be claiming that I have been bought off, not the other way around.

        By the way, “Ivan”, you don’t even have the guts to use a real email address. I guess you felt that was funny or something. Instead it’s just gutless.

      • doritmi March 31, 2017 at 18:23 #

        Yes, every product licensed by the FDA needs to be tested and studied before licensing.

        By the company that developed it. That’s not the CDC.

        If you want the CDC to do a specific study, that does take money. If it’s a study with no good justification, special funding might be needed.

  3. Pik Chu Wong April 18, 2017 at 00:56 #

    A vaccinated vs unvaccinated study is by no mean simple or cheap, but it doesn’t mean it is not needed before releasing a product that will impact millions of lives. The vaccine product should not be release without fully understanding the short term and long term impact. Our immune system is nothing to be messed around with since a healthy immune system is our best protection again viruses and disease. We should not take the approach of give us the funding and the directive to do the necessary studies.

    • Sullivan (Matt Carey) April 20, 2017 at 15:40 #

      If you are asking for a prospective study, you can add unethical to your list of reasons why it is not easy to do a vaccinated/unvaccinated study.

      We have multiple studies on the specific question of MMR and thimerosal and autism.

      Do you accept that neither of these increases autism risk?

      Unless you do, asking for another study is asking for what is almost certainly a waste of money. If you can’t be convinced by the data that exists, new data will be meaninglesss


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