Foundational Reading

The most valuable books in my battle to recover from Lyme disease and co-infections

The Beginning of Infinity: Explanations That Transform the World (2011) by David Deutsch delivers a superb presentation of how we create knowledge — which Deutsch identifies as effective explanations — and how we should evaluate the quality of claims that we might encounter. I particularly take to heart Deutsch’s Principle of Optimism: “All evils are caused by insufficient knowledge.”

Current mainstream medical practice — dubbed “Medicine 2.0” by Dr. Peter Attia¹ — is woefully inadequate when deciding which treatments to pursue in order to combat a mysterious, complicated illness. Medicine 2.0’s approach is generally symptomatic and relies on observations of what has tended to work on average — not necessarily what will for you individually. Medicine 2.0 views randomized control trials (RCTs) as the ideal, but RCTs steer knowledge away from explanation and instead toward mere associations of input and output.²

Effective treatment arises by first diagnosing — explaining — the cause of illness, and, to the degree possible, deducing what will eliminate or at least ameliorate that cause.

Deep Nutrition: Why Your Genes Need Traditional Food (2017) by Catherine Shanahan, M.D. I actually started eating along these lines a few years earlier, guided by Perfect Health Diet (2010) by Paul Jaminet, Ph.D.; if forced to pick, I’d favor Dr. Shanahan’s book because it’s more comprehensive. Two personal observations:

• Years before contracting Lyme disease, arthritis forced me to quit karate and reduce running mileage. Ending consumption of heated and refined seed oils has eliminated pain in my knees and shoulders. … Recently, while taking a shower I noticed a tube of Clearasil Daily Face Wash and realized I hadn’t used it in years. The use-by date on the tube was May 2016, about a year after I began carefully reading ingredient labels and completely stopped ingesting inflammatory oils.

• Substantially reducing simple carbohydrate consumption has improved my ability to sleep through the whole night without needing to get out of bed to pee. (It’s also dramatically reduced my triglycerides and other lab results.)

The End of Alzheimer’s: The First Program to Prevent and Reverse Cognitive Decline (2017) and The First Survivors of Alzheimer’s: How Patients Recovered Life and Hope in Their Own Words (2021), Dale Bredesen, M.D. I don’t have Alzheimer’s disease, but Dr. Bredesen’s advice is effective for all forms of cognitive dysfunction.

“The fat gene: A genetic mutation in prehistoric apes may underlie today’s pandemic of obesity and diabetes” Scientific American (2015) 313(4):64-9, by Richard J. Johnson and Peter Andrews. A scientific research exemplar: cross-disciplinary fusion explaining a wide array of medical issues and biological and paleontological phenomena. Rick Johnson has since published a few books that I haven’t read yet; based on Rick’s interviews that I’ve heard, I’m sure they are well worth reading.

One thing that’s missing from this list is a book on Lyme disease. I haven’t found a useful one yet! I would love to hear about one if there is.

Technical Literature

The Methodology of Scientific Research Programs (1980) by Imre Lakatos. Deutsch credits Karl Popper with his philosophy of science, but Lakatos — who unfortunately died in his early fifties — assembles a more thorough and accurate account of how to successfully conduct scientific research. Reading Popper can be misleading, and hearing second-hand what Popper supposedly advocated definitely so, because Popper’s thoughts evolved over several decades from positions he later rejected — thanks in no small part from interaction with his brilliant student Lakatos.

Statistical Rethinking, 2nd Edition (2022) by Richard McElreath, Probability Theory: The Logic of Science (2003) by E. T. Jaynes, Mathematical Statistics: A Decision Theoretic Approach (1967) by Thomas S. Ferguson, Statistical Decision Functions (1958) by Abraham Wald, Causality: Models, Reasoning and Inference, 2nd Edition, (2009) by Judea Pearl, The Growth of Biological Thought: Diversity, Evolution and Inheritance (1982) by Ernst Mayr, and Bayesian Data Analysis, Third Edition (2013) by Andrew Gelman, et al. These sources still don’t quite capture my approach to statistical inference, so I hope to one day write the definitive book. 🤪

Breast Cancer and Iodine: How to Prevent and How to Survive Breast Cancer (2001) by David M. Derry, M.D., Ph.D. Dr. Derry’s book covers much more ground than its title suggests, starting with iodine’s role in the development of the first nucleated cells — eukaryotes — through a variety of functions in the human body, particularly the thyroid and general cancer prevention mechanisms; there’s just a concluding chapter on breast cancer. It was recommended to me by my first integrative physician.

1. I’m currently reading Outlive: The Science and Art of Longevity (2023) by Peter Attia, M.D. I really like what I’ve read so far, although I expect to disagree with some of the recommendations further in the book.

2. Coincidentally on the same day I published this article, Experimental Fat Loss stated more emphatically my complaint that RCTs only deliver what works on average:

Due to the religious insistence on randomized controlled trials and using a large number of people for studies, it’s pretty much impossible to find any solutions unless they apply to everybody.

I’ll add one more complaint: in their purest form, RCTs discard the wealth of information generated by an experiment in favor of a single binary bit: yes/no to the question “does the treatment work?” Especially when conducted in conjunction with frequentist null hypothesis testing.