Bernalillo County, NM

Infected: 1970s
Diagnosed: 2013
Current health: “Much improvement on long-term antibiotics, but still struggling.”

Chronic Lyme is like stepping through the looking glass straight into Hell. –Jonathan Locke

After decades of misdiagnosis and mistreatment, Jonathan’s health began to seriously deteriorate in 2009. It took visits to twenty-three doctors and tens of thousands of dollars in medical costs before he was correctly diagnosed with Lyme disease. “My family doctor simply gave up on me in the end,” he said. “After being my doctor for more than twenty years, she made it crystal clear that she had no idea what was wrong with me, had nobody else to refer me to, and didn’t want me to come back. And this was at a major hospital in Seattle. It’s at moments like these when you realize just how far the medical world really is from coming to terms with Lyme.”

Jonathan is a software architect, a technology writer and the originator of Apache Wicket. He worked on Java for Sun Microsystems and on platform technologies for Microsoft. He says he’s very lucky now to be working for Telenav on OpenStreetMap, which is essentially the Wikipedia of maps. The company has been extremely supportive of his condition, Jonathan says. “There have been times when I had enough trouble with memory and focus that I thought I might eventually lose my job. I make my living by thinking about really complex problems. If this condition affects my brain in a significant way, that would be some very deep water. So, Telenav’s ongoing assistance and understanding has been really crucial to me and I’ve been able to stay employed through this ordeal, at least so far. Not everybody with chronic Lyme is so lucky in this respect.” Here he talks about coming to terms with Lyme and the shockingly complicated world of controversy and confusion that surrounds this disease.

“The most difficult part of chronic Lyme is the rude awakening that most of us get sooner or later that you simply cannot trust the medical community on this issue. Everything is different once you’re diagnosed. Left is right, up is down. And it’s up to you to make sense out of this crazy wonderland on your own — and all while fighting daily battles against severe and disabling symptoms.

“On the one hand, you have the IDSA’s mad hatters, who are supposed to be leading us, but are instead absolutely intransigent in pushing questionable treatment guidelines for a disease that we are only just barely beginning to understand — and they are doing this, by the way, in the face of a rising tide of protest and contradictory evidence from doctors and major research institutions, not to mention an anti-trust investigation that has revealed multiple undisclosed conflicts of interest on their board, a board which further appears to simply dismiss members who have a different view of Lyme disease. And as you go down this rabbit-hole of awakening into the depths of this awful controversy you’ll inevitably start to make connections between Lyme and a whole host of other rapidly growing diseases. And you’ll wonder ‘How much of this is just Lyme?’

“You know, if the CDC says three hundred thousand people are being diagnosed with cases of Lyme each year (according to their very strict definition), what about the other 40% of cases that we know will be false negatives on the near-worthless Western Blot antibody test that is the “gold standard” for Lyme diagnosis today? And just how many more people are sick with Lyme and have no idea what’s wrong or, far worse, are being treated for something else (ALS, MS, Alzheimer’s, CFS, fibromyalgia, autism, cancer, basically any systemic problem with immunological and/or neurological involvement)? And, is the total number of people infected each year closer to a million or is it maybe even as high as two or three million? It will really start to make you wonder and you will definitely see people around you who either have it for sure or might have it and just don’t know yet.

“While a lot of this train wreck is hard to look away from, on the other hand, it’s not all a conspiracy and not everybody has Lyme and it’s important to keep some perspective and also to understand that there’s just so much terrible desperation out there (and if you have neurological Lyme you will eventually be desperate), that there are doctors and patients doing questionable and really scientifically-unsupportable things. And they’re actually doing these things not because they are quacks or loonies, but because they’re just out of ideas, and because the pain and the exhaustion and the disability and the sheer misery just won’t stop. You know, you’ve got all these patients who don’t know what to think because of the hysteria and disinformation being created by the IDSA, and so they go with their gut and refuse antibiotics (which in some cases may be their only hope), and these patients when they get sick enough will eventually be making a choice between suicide and spending their last nickel on hydrolyzed silver IVs or bee venom therapy or Rife machines or getting deliberately infected with malaria (none of which probably does anything for anyone!). But if you’re that person, what are you realistically going to choose? Even bee venom therapy is probably a better alternative to suicide. You never know, in spite of all evidence to the contrary, it might work.

“So, it’s actually very logical when you think about it that there’s a lot of really crazy stuff going on out there. This is what happens when the people who are supposed to be leading fail to lead. And so it can be a real trial to choose your own path through this mad tea party — to figure out which way is up, which ideas matter and which ideas are total bunk, and which doctors have at least some idea what they’re doing and which are just completely lost in the woods.”


As a software developer, Jonathan is working hard in his spare time to “hack on Lyme”. He’s taking Bioinformatics from UCSD and Machine Learning from Stanford, reading research papers and watching biology videos on Khan Academy. He’s even beginning a new Open Source library for bioinformatics, although he emphasizes, “It’s just baby steps right now. I learn best by modeling complex things in code and my understanding is still very limited.” He says it’s his hope to support the missions of Lyme non-profits like Bay Area Lyme until he can eventually make more direct contributions in a laboratory that is working on unraveling the mystery of Lyme disease.

6 Comments on “Jonathan Locke

  1. Maybe it is also interesting for you to look at the work of professor Dale Bredesen. He is an Alzheimer researcher and it seems like he has developed a successful approach in treating pre- and early Alzheimer’s disease. He identifies 3 types of Alzheimer and a third one manifests differently. In my words: not so such in memory but more in organizing, probably also focussing. And also he mentions people losing the ability to solve complex things, loosing the ability to do math.I think he also mentions that these are actually different diseases but because amyloid beta is produced in the brain it is called Alzheimer’s disease.

    He relates that third form of Alzheimer’s disease to toxins. Bio toxins (like mold), or things like mercury, but maybe also physical toxins (a physical toxin could be EMF). Wireless radiation and also radiation due to dirty electricity. Dale Bredesen mentioned in an interview, if I recall correctly, that EMF is a possibility but that more data is needed.

    From a scientist perspective it is maybe too early to make definitive conclusions about this but from a personal perspective you can just try out simply strategies to eliminate exposure to it and see if this improves the situation after a sufficient amount of time (like maybe a month or several months).

    In one lecture he also mentioned Lyme, but if I recall correctly he related that to inflammation in the body. But as far as I know, inflammation is related to the first form of Alzheimer. On the other hand the human body is very complex so maybe Lyme impacts the body in several ways. He also indicates that often multiple factors are involved.

    His approach may be interesting to you. It may not remove the cause of your problem but his insights may help to support your brain in this situation. For example, a certain diet may produce ketones in the brain and if due to Lyme or other factors amyloid Beta is produced in the brain, the brain cells affected by this can use ketones for energy while because of the amyloid beta they have a problem using glucose for ATP production. The ketogenic diet may not solve the cause of the problem but it may help your brain to function better in this situation and this may help you in your job and daily life.

    This ketogenic diet is not an easy diet. You have to eat more fat and less carbohydrates and also eat more salt and maybe also supplement with other minerals. It is probably a good idea to read books about it like books by professor Jeff Volek and/or Dr Eric Westman because these people have lots of experience with it.

    In addition to this diet things like mct-oil (c-8 oil) might be interesting because the body makes more ketones when these fats are consumed. Maybe also in addition to the diet, exogenous ketones may also be interesting. These are in the form of salts but recently also a ketone-ester product was presented, see here.

    His program also includes other things like exercise, sleep, intermittent fasting, circadian rythm, supplements etc.See these presentations for more information:

    Reversing Alzheimer’s Disease – Dr. Dale Bredesen, MD
    https://www.youtube.com/watch?v=6D5aA_-3Ip8

    Reversal of Cognitive Decline
    https://www.youtube.com/watch?v=QqQ_X3mD16U

    And see also his recently published book:
    The End of Alzheimer’s: The First Program to Prevent and Reverse Cognitive Decline

    This is a presentation by professor Jeff Volek, PhD, RD, on ketones: Ketones: From Toxic to Therapeutic to Ergogenic

    See also this presentation,‘Optimising Weight and Health with an LCHF Diet – Part 1,’ by his co-author, Dr. Stephen Phinney, in which he also explains why it is necessary to eat more salt on this diet.

    For more information about the effect of wireless radiation see the presentations by professor Martin Pall and also a presentation by Magda Havas, she is also a professor.

    How wireless technology harms people and nature – Professor Martin Poll

    Dr. Magda Havas – Presentation

    In the presentation below Martin Pall suggest a mechanism by which microwave radiation might harm cells in the body. He mentions that so called voltage gates calcium channels are opened by microwave radiation and due to that too much calcium ions enter a cell and this results (among other things) in the production of free radicals which can damage the cell.

    See also Mada Havas’s youtube channel for more information on things like wireless radiation and dirty electricity. Dirty electricity is produced by certain electronic devices such as CFL (compact fluorescent Lamps) so I replaced these with halogen lamps (which also have a more natural light spectrum which includes near infra light which might have positive health effects).

    https://www.youtube.com/user/magdahavas/videos

    Maybe you are also interested in the work of professor Nathan Price and his colleagues. Like in Dale Bredesen’s approach they measure a lot and even more than in the approach of Dale Bredesen and use mathematics and computersoftware to analyse large sets of data.

    See these presentations by him:

    2017 Exploring Frontiers | Nathan Price
    Systems analysis across neurodegenerative disease and cancer

    A 100k Wellness Project by Nathan Price, PhD

    By the way I actually used the Wicket webframework in the past and I am still using it in an application in addition to other frameworks like Spring and Hibernate.

  2. I really don’t know enough to answer this question, I’m afraid. I do think there are multiple genetic factors at play. MTHFR and HLA-DR mutations appear to have some correlation (I have both and quite a bad one wrt HLA-DR, which is I believe already known to correlate with MS). It would be good to ask Bay Area Lyme about this as they work with researchers much more directly and know much more about this topic. I’m more interested student not a researcher or doctor. Best luck.

    1. Please note: genetic differences from both the pathogen and the host (here, humans) could play an important role in disease progression. Cytochrome P450 is a known enzyme which could affect both drug metabolism and disease by affecting inflammatory pathways. Cytochrome P450 variations are common and can certainly be important when looking at tolerance or risk of adverse reactions to various medications, as well as general ability to detoxify, process hormones, process neurotransmitters, etc. However, there is only a small body of research on this aspect and other than looking at certain medications and the pathways through which they are metabolized, there are not a lot of specific clinical recommendations that have been generated from this information. General measures to support liver, gallbladder, and gastrointestinal function are important in all patients with chronic disease, and probably more so in people who have known variations or mutations in liver detoxification genes. Bay Area Lyme has supported research looking at genetic differences and the role it might play in disease in mice. This would help inform and prepare for human studies. (See research by Vincent Tam, PhD, “Lipidomic Profiling of Bioactive Lipids by Mass Spectrometry During Microbial Infections,” here.)

  3. Hello, I am reading that you take Bioinformatics ….my son was also diagnosed with Lyme disease and I was wondering if there is a connection between Lyme & co-infections and Cytochrome P450 (and phase 2 conjugation)? [My son] got tested at Genelex in Seattle and has a few CYP polymorphisms. Any suggestions? Thanks, Birgit

    1. I’m sorry to hear it. I have no doubt about what you say, although there may be more than just Bb capable of causing these things too. A couple years of treatment and I’m doing much better with no pain and little fatigue, but my remaining symptoms are now indicating the Babesia duncani co-infection we just recently confirmed, is dominant.

      We desperately need more doctors to understand where this is now and where it is likely going because otherwise they won’t understand the gravity of the situation. We can save lives and many billions in damage by taking this seriously for a change.

      Please keep spreading the word.

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