LYMEPOLICYWONK: More on Who’s Who and What’s What – NIH Dr. Phil Baker Responds to Blog on American Lyme Disease Foundation

26th March 2013

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Last week, I posted a blog regarding the IDSA stealth front organization, the American Lyme Disease Foundation (ALDF). I pointed out that the organization masquerades as a patient organization or an independent source of information, but is really just the members of the IDSA Lyme guidelines panel and a couple of businessmen. I highlighted the fact that Dr. Phil Baker who was responsible for overseeing the Lyme clinical trials at the NIH prior to his retirement is now the Executive Director at the ALDF. I also raised questions about his management of two NIH trials under his watch, the Klempner trial and the Embers trial. Both trials were funded around the same time. Klempner, which concluded that chronic infection did not persist and that treatment was ineffective, was published in 2004. Embers, which found persistent infection notwithstanding treatment, was not published until almost ten years later. During the interim, the Klempner trial was relied on by the IDSA to deny patients treatment for chronic Lyme and no one mentioned that the companion study, the Embers trial, was still pending. Dr. Baker took issue with my post (see below), and I respond.

Dear Ms. Johnson:
Once again, without providing any evidence whatsoever, you claim that publication of the results of Dr. Mario Philipp’s  non-human primate studies were delayed for 10 years. [Dr. Phillip was the primary investigator on the study, but Dr. Embers took over as lead author on this study] By whom? I challenge you to ask Dr. Philipp confirm that was indeed the case and to present supporting evidence to substantiate such a claim. It is time that we hear what he has to say on this matter.

I’m sure that you, as a lawyer, appreciate the serious nature of making claims such as this, without adequate documentation.


Phillip J. Baker, Ph.D.
Executive Director, ALDF

My response follows.

Dr. Baker:

 My point is not who delayed the study or why it was delayed. I am holding you accountable for something even more important — for not accurately conveying to the public the state of the science during the ten year period the study was pending. The Embers study was specifically designed as a companion study to Klempner using direct detection methods unavailable to Klempner to determine persistence.  Until the Embers study was published, you should have urged caution to those (the IDSA in particular, recall that Klempner was one of the guideline authors) drawing overly broad strong conclusions from Klempner to support denial of care to Lyme patients.  Instead of telling people there was no need for further studies and that the science was all in on chronic Lyme disease, you had an obligation to tell the public that studies were still pending, that the state of the science was “uncertain”, and it was too early to draw strong conclusions.  The damage that has been done to the Lyme community and to Lyme science by this rush to mischaracterize the Klempner trial as a conclusive study is immeasurable.

The current state of the science in Lyme disease is “science-in-the-making” and acknowledging this provisionality is an essential feature of scientific integrity. Science is supposed to be truth generating, but this can only happen when there is a free market of ideas and when contradictory viewpoints get a fair hearing. Scientific truth suffers when people or institutions within democratic societies “get hold of some institutional position of power (a scientific journal, a research institute)” and impose their favorite “line” of research there, leading to a dead end.”(Labinger 2001; pg. 46.)

Here, rather than holding the line on scientific integrity, in my opinion, you threw in your lot with the dogmatic views of the IDSA, a medical specialty society pursuing a Lyme agenda that was not in the public interest.  This agenda included advocating against its competitors legislatively and through medical board hearings, hoarding the lion’s share of Lyme research funding for its panel members, and promoting the dominance of its Lyme guidelines.  You had an obligation to the public to remain impartial and to not promote the views of a private organization with a private agenda.  Instead, as your current position with the ALDF makes clear, you became a partisan advocate for the IDSA and officially joined their front organization when you retired.

The LYME POLICY WONK blog is written by Lorraine Johnson, JD, MBA, who is the Chief Executive Officer of, formerly CALDA. Contact her at

 You can read my prior post, here.


Labinger J, Collins, H, editor. The One Culture?: A Conversation about Science. Chicago: University of Chicago Press; 2001.


13 thoughts on “LYMEPOLICYWONK: More on Who’s Who and What’s What – NIH Dr. Phil Baker Responds to Blog on American Lyme Disease Foundation

  1. I am truly at a loss to understand Dr. Phil Baker’s complaint. He quibbles about lack of evidence to prove the Embers study was delayed, even using vaguely threatening legal language. But the time between when the study concluded and when the results were published was nearly 10 years. How can this be in dispute? His lack of attention to the points of the original article speak volumes.

    Lorraine Johnson – I find your reply to be very well stated. Thank you.

    Dr. Phil Baker – I would like to know how you can continue to insist that persistent infection isn’t possible in humans, when multiple studies have proven it in mice, dogs, and monkeys.

    And how can you be so confident that there is no persistent infection in humans when there is no evidence whatsoever to prove a cure? Absence of proof is not proof of absence, especially in a patient whose illness is unresolved and even worsening.

    How do you justify such rigid loyalty to an opinion based on a single highly flawed study (run multiple times) that only proves that a second month of treatment fails to resolve all symptoms of still suffering Lyme patients, which is consistent with those who say these late stage patients need 1-2 years of treatment?

    How can you dismiss Dr. Leigner’s patient in the 1990′s whose tissue samples were confirmed to have Borrelia spirochetes after many months of IV Rocephin, and whose blood was used by the CDC as a known Lyme patient? Is this not scientific “proof” of persistence in opposition to the IDSA’s and your opinion?

    How do you justify ensuring that no NIH funding went to researchers who wanted to prove persistence, especially given the loud and growing outcry by suffering patients and their treating physicians? You have previously insisted that those who want to challenge the official position must prove their claim.

    I think you could become a beacon rather than a lightening rod to the Lyme community if you were to tell the whole truth and dedicate your future to helping people sick with Lyme Disease get the diagnosis and treatment they should get. The devastation to patients’ and their families’ lives in the last 15+ years is incalculable, and it’s only getting worse.

    The truth will eventually come out, as did the stories of germ theory, h. pylori, and AIDS. This is a history making story in its scope and its depth of remarkable suffering. It is still hard to comprehend that this is happening in America today. How will you be remembered in this story? As the champion of patients seeking a cure from a devastating illness? Or as a primary obstacle to those patients?

    Because after all, medicine is not primarily about studies or grants or patents or committees. Nor is it, or should it be about the careers or reputations of anyone. It is primarily about the well being of the patient sitting in front of his or her doctor. The further the focus gets from the patient, the more our medical system will decline and the less adaptable it will be. “New” diseases will continue to run rampant while we lose precious time waiting for the experts to change their opinions or overturn cherised, long taught “truths.”

    • Dear M.T.,
      Thank you so very much for your compassionate and empathetic words. I very much appreciated your thoughtful, encompassing response. Thank you to Lorraine for being the enduring advocate.
      So many have lost their lives to this illness through despair, bankruptcy, fatigue, lack of understanding and compassion, and many family and friends have had to stand by through the suffering, feeling impotent to help. This needs not to be about ego our shutting down creative solutions and research but about a strong and continued effort to find answers for the betterment of the world. I have taken the prescribed IDSA’s dosage of antibiotics to cure this illness, and I am living proof of persistent infection add I have just received a positive blood culture for Borrelia. We do not have all the answers and it is ultimately frustrating to someone suffering and struggling, when someone, not standing in your shoes, can profess to knowing without a doubt that things are as they perceive.
      Thank you for your enduring push for truth.
      In deep gratitude,

  2. Nailed it!!! Nice job of not falling for Baker’s misdirection. I wonder what it is that drives someone with a scientific background to jetison the truth in favor of partisanship, and to trade their career in science for one as a PR flack and lobbyist.

  3. A brilliant lawyer/MBA who is a Lyme survivor and advocate, AND she’s on the side of truth. You have no idea how much we Lymies appreciate what you do. Thank you. Again.

  4. Patients who have done their homework know the truth about the ALDF. They are not telling the truth about tickborne diseases and apparently don’t care how much damage this does. I find it incredible that people who obviously know better could keep doing this kind of disservice to public health. In any other field, they would be charged with crimes and put in jail.

    Every time I pay my taxes, I wish I could opt out, citing the money that is being wasted by the NIH and CDC in their mishandling of this epidemic. What kind of response will we get in future when more new diseases crop up if this is an example of their standard operating procedure?

  5. Absolutely outstanding commentary Lorraine!

    Thank you so much!

    “A small body of determined spirits fired by an unquenchable faith in their mission can alter the course of history”


  6. For Lorraine Johnson…

    For “Dr.” Phil, not a MD, Baker…

    Phillip Baker was the former Lyme Disease Program Manager for the NIH. His job was to allocate funds for Lyme disease “research.”


    Willy Burgdorfer, Ph.D., M.D., and Scientist Emeritus at the National Institutes of Health (NIH). Dr. Burgdorfer is the discoverer and namesake of the spirochete (a type of bacterium) that causes Lyme disease, called Borrelia burgdorferi.

    “The controversy in Lyme disease research is a shameful affair. And I say that because the whole thing is politically tainted. Money goes to people who have, for the past 30 years, produced the same thing—nothing.”

  7. Can’t you smell his haughtiness in his email? Bravo Ms Johnson for refocusing the argument with class and clarity. How dare he try to sidestep the heart of the matter with semantics and legal threats. Of course you’d never fall for that bait! :) We will not be marginalized! It’s just a matter of time before the truth is exposed. Thank you to the brilliant researchers and tireless advocates like Ms Johnson who keep cutting edge tick borne research in the public and medical spheres.

  8. “Denying persistent and/or recurring Lyme disease” – a crock of a waste of time, money, innocent children’s, and others lives.

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