Dr Sidney Baker

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“From a world class healer, Dr. Sidney Baker explains how to think and approach diagnosing and treating any disease – with autoimmune in the later part…”

October 6th, 2017

In August, I had the true and great pleasure of interviewing Sid Baker. I could not think of anyone that could best kick off P5 Protocols than this sage of pure human, medical and life wisdom. His background and evolution to his current thinking, which by the way, despite being near 80, is still evolving, ever learning, reminds me of Charlie Munger, another sage of life and worldly wisdom. When you listen to his history, it is immediately evident that he didn’t take a linear approach to his education nor his life. What continues to make him so fascinating to me is his desire to upset his own apple cart and seek out new approaches, openly accepting that someone else may have a better way. And this comes from one of The Godfather’s of Integrative Medicine! A valuable lesson in humility. But then again, great people provide lessons by their behavior and actions, i.e. by example.

Whether you are listening for direct medical advice on autoimmune conditions or autism, or whether you want to understand how to develop or refine your approach to your own or your patient’s or loved one’s path through health, OR even if you are in business or need life advice, the parallels between how he sees medicine and life can be of great value. I have now listened to this recording several times more than I needed to get the notes done. I could go on in my praise, but instead of me telling you, I think his words will show you, which of course is a better approach to teaching and learning.

If you are looking for protocols, or what I would term adaptable protocols for health, there are some in the latter half of this interview; however, the direction we took was more broad but also sets the stage for how any one person can manage any illness or approach to peak health, including what s/he should demand from her practitioner or him/herself .

Dr. Sid has that sparkle in his eye that be-tells of his kindness, passion and curiosity and desire to get his patients healthy! To have done everything he can for his patients! Despite his soft-spoken-ness in this podcast, I am sure you will sense that sparkle and strength. And with that, here is Dr. Sidney Baker…


For those of you with material time constraints, below we have tried to provide you with the most succinct yet informative “crib notes.” Thank you to Casey Cunningham who has worked with me on these notes and who I hope will continue to do so in future podcasts!

• Background: Dr. Baker started off as a history major at Yale University.  In between his third and fourth year, he took a year off to travel to the far east with his history professor.  While in Indonesia, he ran into two ladies who told him to seek out Dr. Edgar Miller in Kathmandu.  After writing Dr. Miller to no response, Dr. Baker found his address and waited for him on his doorstep.  This first interaction marked the start of Dr. Baker’s medical career. (1:00-2:44)

• Have We Done Everything We Can For This Patient: Under Dr. Edgar Miller. Dr. Sid was exposed to a unique perspective towards treating patients.  Before leaving every appointment, Dr. Miller would ask one simple question: “Have we done everything that we can for this patient?”  This would shift his way of thinking away from the disease and instead towards the individual.  Patients are individuals while diseases are just ideas.  Doctors in modernized cultures regard diseases as one in the same, and thus ignore the differences between the individuals who have the disease.  Illness can manifest very differently, and doctors do not typically acknowledge these differences.  This is mostly seen in chronic illness, where the doctors are off-kilter with forgetting that every living thing is unique, and therefore every disease needs to be looked at differently, patient by patient.  (2:45-6:10)

• Treating Chronic Illness (6:11-13:53): When it comes to treating chronic illness, there are two simple questions that a doctor must consider. The first one is: “Does this person need something that will help the nature of healing?” In other words, can you support healing by finding an ingredient that the patient has a special need for. An example of this would be a patient who had an unmet need for Vitamin D. Once this patient fixes his or her Vitamin D deficiency, then his or her health will improve. In contrast, the next question asks: “Does the patient need to avoid a particular ingredient to feel better?” An example of this would be toxins, which are poisons that have a diverse set of side effects depending on the individual. These questions emphasize the importance of treating the individual instead of treating the disease.

• New Perspectives And A Broader View of How People Heal (13:54-22:49): Dr.Baker was inspired by a man named Milton Sand, who worked as a psychiatrist at the Yale Children’s Center. His work with Dr. Sand influenced his decision to complete residencies in pediatrics and obstetrics. When opportunity struck, Dr.Baker decided to once again take time off from Yale and complete a two year term with the Peace Corps in Chad, Africa, where he saw thousands of patients. While in Chad, he was astounded by how healthy the population seemed to be in comparison to modernized countries like the United States. He later found out that these healthy looking individuals in Chad all had traces of Malaria in their systems. This offered a different perspective on the modern definition of “healthy”. While many individuals were infected with Malaria, it was rare to see anyone with the chronic diseases that plague patients in the United States, including no allergies nor autoimmuneHe concluded that this was due to a lack of germs in the digestive tract which resulted in a loss of tolerance of the immune system. The patients in Chad had germs in their digestive tracts, which helped them tolerate disease and ultimately resulted in a chronic-illness-free community. Tolerance and diversity are important in all systems.

• Assistant Professor of Medical Computer Science and Family Doctor (22:50-27:05): After completing his Peace Corps term, Dr. Baker returned to Yale as an Assistant Professor in Medical Computer Science. This type of technology is crucial for helping patients and doctors alike reveal health patterns. But after a few years, he went back to practicing medicine in a community pre-paid health plan system in New Haven as a Family Doctor for seven years. Through his experiences, he heard many stories from the patients that were different than what he was taught in medical school.

• At the Gesell Institute and beyond, including the TACKS rules (27:06-31:56): After seven years, Dr. Baker went back to being a regular doctor and focused on teaching and writing books on his experiences. While doing this, he contributed to the beginnings of what is now known as functional medicine. The basic principles of this included the “get and avoid” verses the “name it, blame it, tame it techniques that were commonly used in medicine. TACKS rules include if your sitting on a tack, it takes a lot of aspirin to make it feel good! If you’re sitting on two tacks, removing one does not make it feel 50% better. This functional medicine movement aimed to encourage other doctors to view chronic illnesses in a different perspective. This patient focused movement aimed to constantly tweak what patients were doing in an aim to remedy their illness without impeding too much into their everyday lives. However, this led to the risk of common sense, which worries not about techniques working, but about offending other established colleagues in the process. These radically new approaches to medicine go against the orthodox system of thinking. The risk of common sense is not so much that it doesn’t work, but that it offends another professional who sees it as a heresy…. Heretics were burnt at the stake.

• Our System Was Built for Acute Illness, Not Chronic Illness (31:57-40:01): The current system of thinking (get and avoid and name it, blame it, tame it) works incredibly well for acute illness. However, the shift of treatment methods have lagged behind the massive shift from acute to chronic illness. Further, the language has not shifted for the increasing prevalence of chronic diseases. In order to effectively treat chronic illness, doctors need to consider balance, individuality, and control. By putting a name on the problem, you give the patient a fleeting sense of control. However, this is not a permanent fix, which makes it imperative for doctors to collaborate with patients (and with children andtheir parents) when discussing potential treatments. Don’t just do what the doctors say. Autism as an example. Best practices engage everyone…. “I’m not a doctor is not a good reason not to think. If it’s common sense, we are thinking about, then it is OK if you’re not a doctor. If you’re a parent, you can come up with ideas that may be right on target because you’re a mom, especially moms… who often have remarkable intuition…. Women in general have the quicker link to the source of good ideas and they should be listened to….”

• His Protocol / Process for Treating Autoimmune Diseases (among others) – Dr. Baker objected to protocols as a term because it implied standardization, so I Coined Them Adaptable Protocols – a middle ground? (40:02-1:07:43):

o When he starts with a patient, he salutes the “top of my totem pole,” which is filled by Yehuda Schoenfeld, an Israeli immunologist – “arguably the leading immunologist in the world.” [see links below]

o The main portion of the podcast thus far has focused on establishing Dr. Baker’s treatment approach. Now he talks about how he executes these methods when treating patients. He says that when the immune system is inflamed, that is a key indicator that the patient has lost its immune tolerance. In order to restore tolerance, one must expose it to certain germs.
o Introducing new ways (@ 44:00) – SIMPLE approaches and thinking. It doesn’t have to be that complicated.

o Paraphrasing a Quote from Yehuda Schoenfeld @46:00: Until proven otherwise, all chronic illness is autoimmune due to your body taking exception to its own…. But in Schoenfeld’s book (The Mosaic of Autoimmunity), he says that after you read the chapters by 52 top immunologists that you will think all chronic disease is infectious – including autoimmunity. That bugs, infectious agents, bacteria, viruses are the underlying target for all of these inappropriate reactions in which the body becomes inappropriately sensitive to something in your own body, in the air you breathe or the food you eat that it takes to be an enemy… To establish this loss of tolerance. He includes Alzheimers, heart disease and others though not yet widely known as such.

• First try getting rid of yeast and see if that helps.
• Helminthic Therapy – Worms – which freak us out, but our kids pick up nastier bugs at school. Back to Africa when he was young where he saw many people with worms who were the picture of health. But it is not marketable! After running an experiment with HDC’s (whip worms) in the digestive tract, Dr.Joel Weinstock at University of Iowa gave TSO’s (another worm) and half the severely ill patients recovered. He is now at Tufts Medical Center. See links below. helped restore tolerance for many patients at the University of Iowa. Pig farmers do not get autoimmune disease. However, due to nature of medical decisions, this HDC method will not be endorsed by Big Pharma and the FDA. Yet Dr. Baker argues that if the stakes of immune tolerance are high and the costs are low, why not try the practice? For any auto-immune. Note that I (David) tried it for about four months and while I initially saw a material benefit, in the end, it did not have a material affect on my health.

Five Considerations – The BROCS (@55:00)
• B is for Benefit
• R is for Risk
• O is for Odds (that it will work)
• C is for cost
• S is for Stakes – Thinking: If stakes are really high and risk is 0 then you go for it – even if it is a 1 in 100 shot and if Odds are 50/50 then that’s a real bargain!
So listen to ads on TV for Humira and others and compare the risks and complications to helminth therapy. David: then throw in that common sense!

o See William Parker at Duke – link below
o So, get rid of yeast and add HDC’s as first / second round
o Restoring tolerance as a form of immunotherapy – but in most cases it historically has been to suppress the immune system as opposed to this track that is to increase tolerance
o The HDC’s only stay in you for a week or so. He believes before they leave, they have a “conversation” with the immune system and their microbial neighbors and the immune system gets more tolerant. In his over 50 years as a doctor, he has seen the best benefits from these HDC’s of any treatment he has ever seen.
o Book: An Epidemic of Absence by Moises Velasquez Manoff.

• To conclude, Dr. Baker reminds listeners that the ultimate goal is for every individual to be at peak health. As a doctor, he has an obligation to continue until the patient is healthy. His endless curiosity led him down the road to practice medicine in a way that aims to treat the patient, and not just the disease. (1:07:44-1:09:07).

• People Mentioned with Links to other Content (and note that I strongly recommend that if you find a person and topic of particular interest, GOOGLE THEM! And if you find something of interest that you want to share, please email us!:

o Sidney Baker
• Asprey interview
• Youtube
• Books: Start with Detoxification and Healing. https://www.amazon.com/s/ref=nb_sb_noss?url=search-alias%3Daps&field-keywords=Sidney+Macdonald+baker&rh=i%3Aaps%2Ck%3ASidney+Macdonald+baker

o Joel Weinstock


o Yehuda Schoenfeld – quite frankly, the best thing to do is to google his name. His publishing and lectures are extensive

o William Parker at Duke – See his papers and other links at is Duke  https://surgery.duke.edu/faculty/william-parker-phd

o Moises Velasquez Manoff
• Book: An Epidemic of Absence – https://www.amazon.com/Epidemic-Absence-Understanding-Allergies-Autoimmune/dp/1439199396/ref=sr_1_1?ie=UTF8&qid=1507247528&sr=8-1&keywords=An+epidemic+of+absence

o Others mentioned
• Dr. Edgar Miller
• Dr. Milton Sand


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