Bacteriality — Exploring Chronic Disease

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Update on tone and other issues

My Fellow Superorganisms,

Those of you already familiar with the site may have noticed I’ve taken down quite a few pieces. Many of these were written about three years ago. I still stand by their general content, but want to make sure they are completely up to date before I put them back up. A second factor in their temporary removal is that, in retrospect, the tone of these pieces is stronger than the tone I would use today.

When I started this blog, I was writing as an advocate and, over time, I’ve evolved to think and write more like a scientist. I want to make sure that nothing that should be described as a hypothesis comes off in my previous writing as sounding like an established fact.

Just so readers know, the vast majority of the information and studies discussed on this site have now been repurposed as part of content for Autoimmunity Research Foundation’s Marshall Protocol Knowledge Base, which I would encourage you to have a look at.


A couple weeks ago, I gave a presentation at the International Congress on Autoimmunity in Ljubljana, Slovenia. The talk was about successive infection and how viruses and bacteria can work together to cause an autoimmune disease state.

Here is a transcript.


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New Policy on Answering Comments

Dear Readers,

It was a tough decision, but I have decided to close comments to posts 25 days after they have been written. For the most part, I truly enjoy your insights and feedback, but I’m extremely busy with my graduate school curriculum and don’t feel that I can offer quality responses to all the comments that come in.

If you have a question to a post that is older than 25 days, post it at The Marshall Protocol Knowledge Base is also a good source for answers.

Thanks for understanding,

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  • A couple weeks ago, I had the pleasure of giving a presentation to a tri-chapter meeting of the Medical Library Association. The topic was why some patients with chronic disease are disaffected and how online social networks have met some of their needs. I try to offer a balanced perspective – both the good and bad of online social networks.

    The live presentation was filmed but the room was a bit on the dark side. So, despite a laudable job filming by my colleague, Judy, I decided to put up a slideshow with voiceovers.

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    Sun-blocking culture among the Chinese

    Not every culture reveres the sun as Americans do. In our recent trip to Chengdu, China with a stopover in Hong Kong, we saw hundreds of people, women especially, blocking light on a daily basis.

    We’re not sure if these people are supplementing with vitamin D (there is certainly no vitamin D added to the food chain!) but they’re certainly not getting a lot of sun.

    The Vitamin D Council insists that people must expose themselves to sunlight and eat vitamin D-fortified products, yet these people are going about their daily lives without any apparent ill effect.

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    Second-guessing the consensus on vitamin D

    Men who have excessive faith in their theories or ideas are not only ill prepared for making discoveries; they also make very poor observations. Of necessity, they observe with a preconceived idea, and when they devise an experiment, they can see, in its results, only a confirmation of their theory. In this way they distort observation and often neglect very important facts because they do not further their aim….

    Claude Bernard, An Introduction to the Study of Experimental Medicine

    This article discusses our experience at the one-day Institute of Medicine workshop on vitamin D and calcium. Both of us had an opportunity to make comments before the committee. Here are Paul’s comments and slides and here are Amy’s comments and slides. Note that our 2009 paper in Autoimmunity Reviews discusses some of the science we allude to in further detail.

    On the cab ride to the IOM committee meeting on whether to change the dietary reference intake (DRI) of vitamin D, Amy practiced her speech.

    The cabbie had been silent for the whole ride, but broke character by talking to us. “So, let me ask you a question,” he said. “Do you take vitamin D?”

    “Actually, no, we don’t,” Amy said. Amy explained briefly how our data suggests that the form derived from supplementation is immunosuppressive, meaning that while it may temporarily improve signs and symptoms of disease, we have found it may do so at the cost of long-term health.

    We asked him if he took vitamin D. He said yes and explained that a few years back, he had a partially blocked artery. It scared him, so he searched the internet and found that high doses of vitamin D were being recommended for cardiovascular disease. He wasn’t clear about the evidence, but in his words, “I had to do something.”

    Which brings us to this point in time. At least in the United States, rates of chronic disease are rising. One recent study predicted that if current trends continue, all Americans will be obese by 2040. Other studies have shown chronic disease is rising at rates faster than could otherwise be explained by an aging population and/or a general increase in population. One recent estimate says that by 2030, 171 million Americans will have a chronic disease. We have to do something, right?

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    Two weeks ago, I boarded a 747 to travel to Beijing, China in order to speak at the 2009 International Congress of Antibodies. Within minutes of hitting the runway, we were greeted by a crew of officials wearing surgical masks and wielding thermometers. The fever analysis was performed as part of an effort on behalf of the Chinese government to ensure that neither I nor my fellow travelers had the swine flu. Luckily I was cleared and proceeded to my hotel which was also the site of the Conference. Before checking into my room, I had to get my temperature checked yet a second time by the hotel staff. I wasn’t opposed to the routine screenings since, at the time, if anyone on my hotel floor had the swine flu the entire floor would be quarantined.

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    Travels, papers, and more… an update

    If I have seen further it is only by standing on the shoulders of giants a pile of driftwood.

    Hello readers!  Suffice it to say I’ve been missing in action for several months.  For much of the time I’ve been traveling.  Some of you may know that I just got back from China where I gave a speech at the International Congress of Antibodies. That will be the subject of my next post when the video of my speech is ready. In the meantime, I finally have time to give you an update of what I was up to before I left for Beijing…just to keep things in chronological order.

    Several months ago I travelled to Vancouver Island to stay with Paul’s brother and his wife. It was wonderful to be surrounded by nature again! We took hikes through 200 year old forests and climbed gnarled driftwood on the beach. It was the first time I’ve sat around a bonfire since getting sick. I even got to take a horseback riding lesson and stayed on the horse!

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    On Monday, I returned from the 6th International Congress on Autoimmunity held in Porto, Portugal. You can watch my presentation here.

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    Three days at the J. Craig Venter Institute

    Though the human genome was fully sequenced in 2001, the most promising work in genomics has just begun and not even in the study of human DNA. Human cells are outnumbered by bacterial cells by a factor of ten to one, and, as the rest of this site alludes to ad nauseam, there is strong reason to believe that bacteria are to blame for many of the chronic diseases from which humans suffer. Genetically speaking, we know relatively little about bacteria that persist in humans. The field is ripe for advances.

    Colorful representations of sequenced genomes adorn the walls at JCVI.

    You may wonder how a researcher can view and understand a particular bacterial genome. On their own, they cannot. Progress in genetics is a group effort, and requires partnering with one of the handful of heavyweight institutions in the world that have developed resources allowing for genome interpretation. Several such institutions exist in the US. The NIH has bacterial protein sequencing tools at its disposal. The Broad Institute at MIT as well as the Washington University Genome Sequencing Center have also developed tools that allow for genome sequencing.

    Many would argue though that the Institution most on the bleeding edge when it comes to genome sequencing technology is the J. Craig Venter Institute, formerly known as TIGR. Headed by transformative iconoclast and entrepreneur J. Craig Venter, the Institute is a non-profit research center that was founded in 2006. It has facilities in Rockville, Maryland and La Jolla, California and employs over 400 people, including Nobel laureate Hamilton Smith.

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    Patient Interviews

    About Amy Proal

    Amy and Zeus

    Amy Proal graduated from Georgetown University in 2005 with a degree in biology. While at Georgetown, she wrote her senior thesis on Chronic Fatigue Syndrome and the Marshall Protocol.

    Amy has spoken at several international conferences and authored several peer-reviewed papers on the intersection of bacteria and chronic disease.

    If you have questions about the MP, please visit where volunteer patient advocates will answer your questions. Another good resource is the MP Knowledge Base, which is scheduled to be completed within the next year.


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