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James Lyon-Weiler and IPAK are running a dubious “vaxxed versus unvaxxed” study

An antivaccine group in Washington is raising money for a dubious “vaxxed/unvaxxed” study for IPAK, James Lyons-Weiler, a bioinformatics scientist turned antivaxer, who plans on analyzing data from a large practice.

Yesterday, as I deconstructed the antivaccine nonsense being peddled by a local “holistic” quack named Dr. David Brownstein in response to a pro-vaccine editorial published by the New York Times last Sunday, I couldn’t help but notice that he invoked one of the hoariest of hoary (and favorite) antivaccine tropes, the claim that there are no “vaccinated versus unvaccinated” studies and the call for one. The reasons that it’s a trope are many, but boil down to a few points. First, those antivaxers who actually call for a randomized placebo-controlled trial of vaccinated versus unvaccinated babies (and they exist) clearly don’t realize that such a study would be incredibly unethical because it would leave the unvaccinated group vulnerable to infectious disease. There is no clinical equipoise in such a study. The other reason is that such a study with sufficient statistical power to detect differences in autism rates between the groups would have to be so large as to be impractical. Also, there already exist “vaxxed versus unvaxxed” studies that don’t show what antivaxers think they show, as well as number of large epidemiological studies totaling millions of children enrolled looking for increases in autism and other health issues that have failed to find what antivaxers think that they should find. Finally, we all know that even a negative “vaxxed versus unvaxxed” study would not convince antivaxers that vaccines don’t cause autism. That’s why I thought I’d finish the week writing about another attempt at mining that trope, which comes to us courtesy of James Lyons-Weiler and the Institute for Pure and Applied Knowledge (IPAK) via an antivaccine group, Informed Choice WA:

Please join Informed Choice WA helping fund THE study the CDC has refused to do.

The public has been demanding this study for decades.

Public agencies have steadfastly refused to fund or conduct such a study.

That’s why Informed Choice WA is so excited to join the grassroots effort to help fund the IPAK 2019 Vaxxed/Unvaxxed Study.

The Institute for Pure and Applied Knowledge (IPAK) is a not-for-profit organization which exists to perform scientific research in the public interest. IPAK is funded by people, not pharmaceutical companies.

Study description from James Lyons-Weiler, PhD , CEO and President of IPAK:

The 2019 Vaxxed/Unvaxxed Study will be conducted with the data from a well-respected practice in the United States that has large numbers of children who are fully vaccinated, partially vaccinated, and unvaccinated. The data is to be analyzed by IPAK, which provides assurance that the study will be regulatory compliant and will be conducted following Institutional Review Board approval. The study design will be based on the feedback and approval from the IRB, and the study will be published following peer review.

When last we met James Lyons-Weiler, he was a panelist at an antivaccine conference. Prior to that, he was battling Leslie Manookian, the filmmaker who produced the antivaccine propaganda film The Greater Good, over who is the most antivaccine antivaccine crank.

The weird thing about him is that he was once a legitimate scientist. He had a faculty position at the University of Massachusetts Lowell from 1999 to 2002 ande established “a Center for Bioinformatics, taught undergraduate & graduate courses (biology, genetics, bioinformatics),” where he helped “researchers w/microarray data and developed web applications for high-throughput data analysis.” Lyons-Weiler then moved on to the University of Pittsburgh, where he remained for twelve years and in 2007 became director of the Bioinformatics Analysis Core there until the core closed in 2014, according to him due to state budget cuts. Now he runs IPAK, his institute where he promotes a range of medical pseudoscience, including antivaccine pseudoscience. (He also likes to refer to vaccines as “filthy, nasty vials of toxic sludge.”)

So can we figure out what he’s doing here? What is this study that he’s asking for money to do? The fundraising appeal mentions “well-respected practice in the United States that has large numbers of children who are fully vaccinated, partially vaccinated, and unvaccinated.” So what does that mean? It reminds me of Mayer Eisenstein, an antivaccine “holistic” doctor in the Chicago area. He had a practice of 35,000 children and claimed that none of his unvaccinated children had autism. However, he died four years ago. So who’s left? Well, there’s also Anthony Mawson, whose “vaxxed versus unvaxxed” study was really just a survey with little in the way of controlling for potential confounders. It was retracted, but keeps rising from the dead over and over and over again. He’s not a physician; so it can’t be him.

It can only be one person, the rising star in the antivaccine movement, antivaccine pediatrician Dr. Paul Thomas. For example, check this out:

I could be wrong about this, but I suspect that I’m not. After all, it’s an antivaccine group in Washington, and that’s where Dr. Thomas’ practice is. Dr. Thomas has been promoting his “study” as the Framingham study of our area, a comparison that never fails to make me giggle derisively.

I also can’t help but note that right now there’s a major measles outbreak going on in Clark County, WA, just across the state line from Portland, where Dr. Thomas practices. He’s basically encouraging parents not to vaccinate while the measles rages just across the Columbia river. Now, it appears to me that he’ll be using those children to promote his antivaccine views, while Lyons-Weiler will use IPAK resources to help him massage the data to show what he wants it to show.

By Orac

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That this particular surgeon has chosen his nom de blog based on a rather cranky and arrogant computer shaped like a clear box of blinking lights that he originally encountered when he became a fan of a 35 year old British SF television show whose special effects were renowned for their BBC/Doctor Who-style low budget look, but whose stories nonetheless resulted in some of the best, most innovative science fiction ever televised, should tell you nearly all that you need to know about Orac. (That, and the length of the preceding sentence.)

DISCLAIMER:: The various written meanderings here are the opinions of Orac and Orac alone, written on his own time. They should never be construed as representing the opinions of any other person or entity, especially Orac's cancer center, department of surgery, medical school, or university. Also note that Orac is nonpartisan; he is more than willing to criticize the statements of anyone, regardless of of political leanings, if that anyone advocates pseudoscience or quackery. Finally, medical commentary is not to be construed in any way as medical advice.

To contact Orac: [email protected]

57 replies on “James Lyon-Weiler and IPAK are running a dubious “vaxxed versus unvaxxed” study”

“The Institute for Pure and Applied Knowledge (IPAK) is a not-for-profit organization which exists to perform scientific research in the public interest. IPAK is funded by people, not pharmaceutical companies.”

As opposed, say, to the NIH which is funded primarily by tax dollars paid by….people.

“Informed Choice Washington”‘s website has responded to the measles outbreak in the state, saying that “most people” don’t have to worry about it, and blaming the outbreak on vaccination.

You see, it’s because the MMR is faulty and adult immunity wanes, making newborns vulnerable, not antivaxers’ fault at all.

You can’t make this crap up.

I’m sure with funding from this group (whose leaders are not identified on their website), and L-W’s Institute for Pure And Applied Bullshit, the vaxed-vs-unvaxed study conducted in the practice of “well-respected” (barf) pediatrician Paul Thomas will come to completely unbiased and scientifically rigorous conclusions.

I just posted an Oregonian article about the outbreak below. It reports that the vaccine coverage in that area is only 66%. That is frightening.

Maybe I missed something; but how does his study differ from some of the other epidemiological studies carried out on much larger cohorts? It isn’t a double-blind randomized clinical trial which would, as you pointed out, be unethical. It is a cohort study, so lots of confounders, i.e., variables related to why some kids in practice got all shots, some shots, none. And if the three groups differ considerably in size, confidence intervals will be questionable, etc. Oh well.

It is different, because all the high quality and well controlled studies failed to show what they believe is true. Mawson’s multiply-retracted survey did come up with the right answer, but embarrassingly it keeps getting retracted as complete dross.

They are hoping this time to produce a new piece of complete dross that people will accept. Either that or the Institute of Pure and Applied Bull$hit is running out of cash.

Oops! I forgot to mention one more problem. Since only one practice which probably chosen for specific reasons by families who more than likely not representative of families in general, so whatever the result it would have NO EXTERNAL VALIDITY, i.e., couldn’t be generalized.

For those not trained in epidemiology, Internal Validity relates to study design, whether groups comparable or not on everything; but variable of interest, in this case, immunizations. External validity relates to whether those in study are representative of whatever group one wishes to generalize to.

As sceptics, it goes against our “ethos” to engage in this sort of prediction. However, It’s kind of sad that anti-vaxxers are so predictably unethical and incompetent that we can reliably do so. I’m certainly looking forward to reading the results of this and applying Lyons-Weiler’s own study scoring system to it.

In case there are readers who don’t already know this: Clark County is part of the Portland metro area. So Dr. Thomas is encouraging parents not to vaccinate their kids against measles while there is a measles outbreak in the metro area where he practices. Keep in mind that there is significant cross-border shopping in that area: Washington has a high sales tax, while Oregon’s sales tax rate is zero. So this outbreak has high potential to cross the Columbia.

It sounds like Dr. Lyons-Weiler has set up a think tank, and like other think tanks, this one is designed to produce reports to support a particular position. I don’t know who’s funding this, but I have to assume (as with the Heritage Foundation and dozens of similar establishments in the DC region) that they are up to no good.

“So Dr. Thomas is encouraging parents not to vaccinate their kids against measles while there is a measles outbreak in the metro area where he practices.”

How do such pediatricians keep their licenses? I can understand why Dr Hickie is so furious.

Believe it or not, I first “met” James Lyons-Weiler right here at RI: he commented about various aspects of vaccination IIRC.
Later on, I noticed that he contributed to AoA or had articles written about him there. He has been a guest at PRN’s woo-fest.
Thus his work may be surveyed for several years.

Three thoughts:
A. If they’re doing that, and want any credibility, they need an actual epidemiologist on board. Lyons-Weiler is not one. Not everyone with legitimate science background is an epidemiologist (I know it’s obvious to the people here). Of course, given Dr. Harrison’s points, none may join them.
B. I think you’re right about Thomas, but I wonder what the outbreak will do to him.
C. Washington state is proposing a limited bill to remove PBEs from measles vaccines.

They might also want a biostatistician, but in my experience they are a hard-headed lot when it comes to study design, meaning they won’t want and wouldn’t get a reputable one, if they get one at all.

Thank goodness on the new bill (limited as it is). I’ll have to write my representatives in support of it!

This current attempt by Thomas is a rather twisted extension of a completely non-peer-reviewed “study” Thomas put into Appendix E of his book “The Vaccine-Friendly Plan: Dr. Paul’s Safe and Effective Approach to Immunity and Health-from Pregnancy Through Your Child’s Teen Years”. He describes three groups of children:

“Group 1: Following Dr. Paul’s Vaccine-Friendly Plan: These children were either born into my practice or establishedcare by the two-month well baby visit. They did not get the birth or infant hepatitis B vaccine. If they got the hepatitis A vaccine, it was after age two. If they got the MMR and chicken pox vaccines, it was at or after age three. There were 1,098 children in Group 1.

Group 2: Unvaccinated: Because of parental choice, these children had no vaccines. There were 238 children in Group 2.

Group 3: Other/ Most Vaccinated: Though there was some individual variability, many children in Group 3 were vaccinated according to the CDC guidelines. There were 894 children in Group 3.”

Thomas then reports no cases of autism in Groups 1 and 2 and 15 cases in Group 3 and states:

“We would have expected to have approximately seventeen cases of autism in Group 3, and there were fifteen autism/ ASD diagnoses, which mirrors the national average. This data demonstrates with a high level of statistical significance that the Vaccine-Friendly Plan— as well as not vaccinating at all— was associated with less autism/ ASD.”

So many holes in the “study” left open it’s not even funny. He does say this “study” is based on 2230 children in his practice from June 2008 (when they first opened) through Feb 2015 and that he was in the process of “compiling the data for a retrospective study approved by the Western Institute Review Board”

Well, it’s clearly never made it any farther than the rear end of his execrable book, so this effart with Lyon-Weiler is probably his next attempt to forge data.

Ah, I see from J L-W’s tweets that he has also become a full “abortion = murder” fetus-licking forced birther.

I’d be curious what we would do if he encountered a rabid bat. Would he deny himself treatment for rabies just because he does not like how the vaccine was made?

Have you seen Adams’ recent abortion-vaccine-toxic sludge/ satanic ritual-demonology material? ( Natural News)

Ah, shoot!
I missed my opportunity to get myself another laughable certificate from a mail order/online scam:
James Lyons-Weiler presents his IPAK 1001 – Anatomy of a Scientific Study online course.
And it was only $150.00 with a “certificate fee of $50.00”
And it is a “Citizen Scientist Course”, apparently accredited by J L-W hisself, but with no accreditation or meaning in the real world.
Those who are taking this farce may as well declare they took a class in BS from my cat and have a “certificate” to prove it.
I wonder if the marks ever figure out that they can achieve the same thing with MS Office or LibreOffice degree/certificate templates… basically for free. Suitable for framing right from their own printer.
They can add any accolades their ego desires and are not limited to the 3 categories Jimmy is pigeonholing them into.
Grifters gotta’ grift and when you have a bunch of lummoxes following you it is almost criminal not to take them for all they’re worth…
This guy is one of the slimiest of the anti-vaccine grifters.
… A worthless “certificate” in nothing for only $200.00 payable to J. L-W.

How much is it to get a degree in BS from your cat? I need all the certifications on my resume that I can get…

“so we can make changes and return to a world where children grow up…without anxiety, learning issues, immune issues or disease.”

Return? Just where/when was it that children grew up with none of those?

This makes me so embarrassed to be from the Northwest. I have grandchildren in Portland (fully vaccinated) and in Clark County (also fully vaccinated).

The measles outbreak in the Vancouver/Portland area is up to thirty cases (though one is in King County, the man had visited the southwest part of the state):

A very scary quote: “If the Vancouver area met what is called “herd immunity,” the number of people who need to be vaccinated to stop a contagious disease, those would be fine activities. But you need a vaccination rate of 93 percent to achieve herd immunity, and as of 2017, the Vancouver area’s was at only 66. That means that people who have never received a vaccine, people who have weak immune systems, children too young to receive a vaccine or people who cannot for a medical reason are in danger of the air itself when they leave the house.”

It reminds me of Mayer Eisenstein, an antivaccine “holistic” doctor in the Chicago area. He had a practice of 35,000 children and claimed that none of his unvaccinated children had autism.

Not to forget the “malpractice charges for killing patients through incompetence” aspect of Eisenstein’s career, or the “fraudulent claims to have malpractice insurance” part, or the “welching on malpractice debts by filing for bankruptcies while fraudulently offering someone else’s property as security” part.

Let us (tinu) not forget his prestidigitation in going from a massive lack of charts to a shiny new, fully stocked computing engine in the space of a couple of years or so.

If some of his patient got autism even when not vaccinated, his or her parents probably changed doctor. His advice was proven wrong.

One interesting component of this study proposal is that these individuals expect an Institutional Review Board to approve this study considering the breadth and depth of currently available scientific evidence. As one who has experience sitting on an IRB committee myself, I would expect any legitimate IRB to voice major concerns for the proposed study – and subsequently deny its approval. I’d be interested to see how the whole IRB process plays out for this proposal.

The way quacks get around this is to have a dubious IRB. For instance, Stanislaw Burzynski’s Burzynski Institute has an IRB run by a crony of his, and Mark and David Geier set up a dodgy IRB to approve their studies. Unfortunately, if the study isn’t federally funded or being done to win FDA approval for a drug or device, there’s not much that the federal government can do about it.

Please explain this video.

Sure. Liars lie and morons believe them. YouTube arose to fill their shared needs. Is that the kind of explanation you sought?

Er, no it doesn’t.
It’s Wakefield pretending that since his co-author Walker-Smith was exonerated, then he is too.
This argument has already been written about here :
As for Justice Mitting “absolutely concurr[ing] with [Wakefield’s] position”, let me quote section 7 of the judgement : “Dr. Wakefield’s statement and subsequent publicity had a predictable adverse effect upon the take up of MMR vaccine of great concern to those responsible for public health. There is now no respectable body of opinion which supports his hypothesis, that MMR vaccine and autism/enterocolitis are causally linked.”

If you read the actual ruling instead of watching a video version of what somebody claims is the video, you’ll get your explanation.

You’re close on Paul Thomas’ location. He’s spreads his misinformation in the Portland a metro area (Beaverton), another lovely hot spot for low vaccination.

I see me reading comprehension failed me. I reread your article- you had him in the right place. I wouldn’t be shocked if WA residents drove to see the darn quack. I live outside PDX and women from my community make the 45 minute drive to see the man so they can follow their intuition to treat their kids, as opposed to sound medical advice.

Update on the stupid, it burns: Arizona state lawmaker introduces bill to make it mandatory to tell parents about all “chemicals” in vaccines.

“Boyer said he’s not necessarily opposed to vaccinations for children and sidestepped questions of whether he personally believes vaccines are harmful.”

“But he said there has been an explosion in the number of vaccines that are scheduled to be given to children, going from five in the 1960s to more than 70 now.”

I take it that this journal does not employ competent manuscript editors, however:

In addition, using our novel approaches and assays

Omit the frosting, please.

I dont get your argument about “it would leave the unvaccinated group vulnerable to infectious disease.” . There are more than enough volunteers for the unvaccinated group.

Did you miss the phrase “randomized placebo-controlled trial”? That means that you can’t use volunteers. The babies would be randomly assigned to either the vaccinated or unvaccinated arm, regardless of what their parents thought of vaccination. To make sure there is no bias, blinding would have to be used.
The second point is, vaccines prevent infectious diseases. That’s literally their purpose, and they do it exceptionally well. Any children in the unvaccinated arm of the study would be at high risk for diseases like Hepatitis, Rotavirus, Measles, Mumps, Rubella, Diphtheria, Tetanus, Pertussis, Polio and HiB. In other countries, they’d be at risk for illnesses like Tuberculosis. All of these diseases can kill, and leave survivors with devastating sequelae like paralysis (Polio), sterility (Mumps), lung damage (HiB, Pertussis and Tuberculosis), encephalitis (Measles) and organ damage (Tetanus).
It is considered unethical to refuse standard treatments except under extremely restricted circumstances. Vaccines are the accepted standard of care (I don’t know if that is the correct phrase). Refusing a treatment and leaving the babies at such risk would be a violation of the Helsinki Protocol.

I still do not see why it would not be ethical. I wouldn’t expect such a well designed study to support antivaxxers, but there have been double blind randomised placebo controlled trials of procedures such as angioplasty in the past. What’s the difference here? Can’t we afford some small population of guinea pigs? After all, people die every day of inadequate care… so I do not fundamentally see the issue here. (The only real issue I really see is that it wouldn’t convince the antivaxxers anyway…)

What if one signed their child up for the study in Clark County, WA, which is now experiencing a growing measles outbreak? They are now in a quandary because they would not know if their child was actually vaccinated for measles.

And if they were an anti-vaccine family, they would not sign up just because they do not want their child to be in the “no placebo” group.

Here is a description of what they really want:

It is unethical and very expensive. Also, totally unnecessary since there have been plenty of large epidemiological studies done over the last twenty years that included unvaccinated children: Vaccines are not associated with autism: An evidence-based meta-analysis of case-control and cohort studies (a pdf of the uncorrected proof)

Sure, I wouldn’t spend a dime on what they want. What I’d like to know, however, is whether or not vaccines have impact on life expectancy, for instance, when neither elements of the groups contract the diseases. I’d just like to know if we could extract information concerning expressions of autoimmune diseases in both groups, for example. Just to know for sure.

As long as herd immunity is enforced, I, personally, couldn’t care less if an antivaxxer’s child dies. Which is fine, since my personal feelings are irrelevant anyway… I would consider it child abuse, though.

Key word is informed consent. If somebody says that he want to have a serious disease, he is obviously not informed.

So, infants can “volunteer” to go unvaccinated?

Now there’s “informed choice”.

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