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Tue, 25 Feb 2020
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Bacon n Eggs

Federal dietary guidelines need to cut carbohydrates

myplate dietary guidelines
This year, as they do every five years, federal officials will publish a new version of the Dietary Guidelines for Americans. These periodic updates to federal nutrition guidelines influence everything from school lunches and military meals to public health initiatives and products developed by the food industry.

In theory, these guidelines reflect the latest, most rigorous nutrition research, but, in reality, they tend to peddle lousy and unscientific advice. Most shockingly, recent studies suggest that the guidelines' central recommendation, that people consume lots of carbohydrates but limit fat intake, has probably fueled the chronic disease epidemic.

Responding to new research showing that low-carb, high-fat diets help people stay healthy, the committee that drafts the guidelines is now considering recommending a low-carb dietary pattern. However, at the end of October, committee members announced that the supposedly "low-carb" pattern they were debating would still encourage people to consume almost half of their calories from carbohydrates.

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I had to start eating meat again for medical reasons, and now I'm questioning everything

BBQ burgers and dogs
"White rice and water," my doctor clarified, after I asked what, exactly, he meant by elimination diet, "nothing else. For three days."

My reason for seeing Dr. Schwartz that day was the same as it had been the past three visits: constipation and abdominal bloating that left me feeling (and sometimes looking) as if I was in my second trimester of pregnancy. I had long identified with the symptoms of Irritable Bowel Syndrome (which I had Googled no less than two hundred times), but Dr. Schwartz insisted on ruling out other gastrointestinal disorders before corroborating my diagnosis.

If the symptoms persisted while I followed the elimination diet, he would refer me to a specialist; if not, and I began to feel better, we would slowly begin adding food groups back to find out how much of each I could tolerate.

Comment: It just goes to show, vegetarianism (and veganism) are often more about group identification and tribalism than health or animal rights. That even when staring down the barrel of serious health complications due to diet has one thinking "but what will my friends think if I change my diet?" is quite telling. If they actually care, it might be time for some new friends.

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Chaga mushroom: This unusual tree fungus is a medicinal powerhouse

Chaga Mushrooms
The mysterious Chaga mushroom (Inonotus obliquus) is a non-toxic, medicinal mycelium with a propensity for birch bark. If you were to spot it while roaming through a birch forest in the Northern hemisphere, you'd probably assume (based on its rather unappealing appearance), that it was some kind of tree infection. But Chaga is a whole lot more than just an unsightly forest blemish.

The chaga mushroom is actually a treasure trove of science-backed healing potential that's been a prominent feature in folk medicine for thousands of years.

Chaga's reputation as a powerful natural remedy for everything from gastrointestinal disease to tuberculosis to cancer spans at least as far back as the 16th century when botanical artisans are said to have figured out that it could be steeped as a tea for a variety of therapeutic purposes.1

The historical record suggests that, even prior to this, natural healers in Asia were likely among the first to document Chaga's medicinal potential more than 4,600 years ago. They observed that the strange fungus has a unique ability to extract nutrients from its hosts and concentrate them into itself. Hence the chaga mushroom's incredible density of B vitamins, antioxidants, trace minerals, enzymes, and more.

Since these ancient times, science has taken our understanding of Chaga to a whole new level, and the West is finally catching on to what this amazing mushroom is capable of. Just in the last century the Chaga mushroom's antiviral, antimicrobial, anti-inflammatory, cardio-protective, anti-hyperglycemic, and anti-cancer properties have become more widely known.

Comment: See also: Chaga mushroom tea: The many benefits of this health-boosting beverage


How to make thieves oil and why you should be using it daily

Thieves oil ingredient
Most of you probably know what Thieves Oil is, but if not have I got a story for you?! The name and recipe for Thieves Oil have an interesting backstory and explains why this blend of oils is so good for you.

The recipe varies and dates back to the Middle Ages where Thieves Oil kept a group of merchants safe from the Black Plague. The mixtures of antiseptic, antibacterial, and antimicrobial properties were able to stave off the Plague and keep these merchants safe.

The Thieves Story

In the early 1990s, Gary Young studied essential oils and recreated a blend he had been researching. According to Gary, there are 17 different versions of the "Story of Thieves" and each contains different amounts of different oils. This intrigued Gary to research essential oils and make the perfect Thieves Oil blend for everyday use.

He researched the properties of the different oils in the multiple ingredient lists he found. His research lead to a proprietary oil blend called Young Living Thieves Essential Oil. His research also lead him to the historical story of the "Thieves" this blend is named after.


Electronic health records prioritize insurance billing over patients and doctors hate them

© Adobe Stock
The House of God, my first novel, was about the abuses of medical internships. After it was published in 1978, it started a conversation that led to significant real-world reform in the way that first year doctors are treated. Our schedules had been 36 hours on call, every third night — sometimes, every other night. The fatigue was hellish. We had no real life outside our job. Medical interns now are prohibited from working such schedules.

Yet somehow the medical profession is worse now. We doctors face an epidemic of burnout. It is estimated that a doctor commits suicide almost every day in the US. More than half of physicians reported symptoms of burnout in a 2014 study, and while that rate dropped to 43 percent in a 2017 follow-up, it is still much higher than the rate for all US workers, which stayed essentially flat in those years. What has gone wrong with our once beloved profession?

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Caffeine has been a boon for civilization, Michael Pollan says. But it has come at a cost

caffeine coffee
Michael Pollan laughs and says, yes, he's on drugs while conducting this interview. Okay, he doesn't use those exact words, but he acknowledges that he has a "tall, takeout container" of half-caff coffee at his side as we discuss, via phone, his latest project, simply titled Caffeine, available only as an audiobook from Audible. (Audible is a subsidiary of Amazon, whose founder, Jeff Bezos, owns The Washington Post.)

Pollan, the author of The Omnivore's Dilemma, The Botany of Desire, In Defense of Food and How to Change Your Mind — in which he has explored our complicated relationship with food, plants, drugs and many other things we take for granted — has turned his imposing analytical skills to caffeine, the most popular mind-altering chemical on the planet.

"For most of us, to be caffeinated to one degree or another has simply become baseline human consciousness," Pollan writes, well, reads in Caffeine. "Something like 90 percent of humans ingest caffeine regularly, making it the most widely used psychoactive drug in the world and the only one we routinely give to children, commonly in the form of soda. It's so pervasive that it's easy to overlook the fact that to be caffeinated is not baseline consciousness but, in fact, is an altered state."

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South Dakota considers first state bill to outlaw all vaccine and medical mandates

South Dakota

Will there be a medical refugee migration to South Dakota?
Who owns your body?

A growing number of legislators in South Dakota believe you do.

They have introduced a bill to not only end vaccine mandates in the state, but all future medical mandates that my be introduced in generations to come.

One hundred and fifteen years ago this month, the US Supreme Court made a decision that because there was a deadly smallpox epidemic, the City of Cambridge, Massachusetts was allowed to charge a pastor five dollars to opt out of a city wide vaccine mandate. The law didn't apply to children.

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The importance of melatonin for optimal health

Sleeping well is an essential strategy to optimize your health, and at the heart of it is your circadian rhythm. This is also known as your body clock. It's a natural, biological timer present in every one of your cells that helps your body recognize sleepiness and wakefulness over a period of 24 hours.

Your circadian rhythm is largely dictated by your pineal gland, located near the center of your brain, which produces melatonin, a hormone that is crucial for the regulation of your sleep cycle.

If you have had enough exposure to bright light in the daytime, your pineal gland typically starts secreting melatonin around 9 p.m.1 As the amount of melatonin in your brain increases, sleepiness sets in as your body begins to prepare for sleep.

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Richard (Bud) Veech, the unknown scientist behind the ketogenic diet, dies at 84

Richard L Veech ketogenic scientist
Richard (Bud) Veech, a biochemist whose research changed our understanding of human metabolism, died, or as he might say, his "great controlling nucleotide coenzymes" reached their final equilibrium on Sunday in his home in Rockville, Maryland. He was 84.

His death was confirmed by his close friends and colleagues.

Dr. Veech spent over 50 years studying the nuances of human metabolism. His work was highly lauded among his colleagues.

"He has redefined our understanding of metabolism," said Dr. Thomas Seyfried of Boston College.

Comment: See also:

Microscope 1

Did Coronavirus outbreak originate in a lab? Novel sequence in 2019-nCoV Virus genome suggests man-made cause

Recombination technology has been in use in molecular virology since the 1980s. The structure of the 2019-NCoV virus genome provides a very strong clue on the likely origin of the virus.

Unlike other related coronaviruses, the 2019-nCoV virus has a unique sequence about 1,378 bp (nucleotide base pairs) long that is not found in related coronaviruses.

Looking at the phylogenetic tree recently published, derived using all the full genome sequence, we see the 2019-nCoV virus does not have clear monophyletic support given the bootstrap value of 75 (Fig 1).

2019-nCoV coronavirus
© jameslyonsweiler.com
Close-up on Bootstrap value of 75 for available 2019-nCoV from Lu et al., 2020 The Lancet article [Full Text]

There is no doubt that there is a novel sequence in 2019-nCoV; we confirmed this via sequence alignment. Here's the DOT plot:

Comment: It's still only a theory, but if it's in the ballpark, then this outbreak could yet be chalked up to madcap vaccine science...

The author posted the following update to his website on February 2nd, 2020:
Dr. Marc Wathelet commented that he was puzzled about my report of a spike protein gene homologous to part of the pShuttle-SN vector, given that spike glycoproteins are found in bat coronavirus. He urged me to analyze the homology (sequence similarity) of the SARS-like spike protein element I reported with other spike proteins, saying that any scientist working on coronaviruses would be surprised if there were not a spike protein.

I replied in comment that I, too, would expect protein sequence level homology due to shared conserved domains, but assured him that I would undertake further genome sequence-level (nucleotide) analysis as the location of the novel sequence relative to the other spike proteins is certainly of interest.

A few recent publications (sent to me by followers/readers) contained further bat coronavirus accession numbers, and SARS accession numbers, so I procured the spike protein coding sequence (CDS) of these from NCBI's nucleotide database and aligned them using Blast, with the sequence from the first 2019-nCoV protein as the anchor. (Oddly, that Genbank entry does not label the S protein CDS as a spike glycoprotein, instead annotating it only as a "structural protein").

The resulting massive alignment confirms a major unique inserted element in 2019-nCoV not found in other bat coronaviruses, nor in SARS in the homologous genomic position:

2019-nCoV coronavirus
© jameslyonsweiler.com
This is why full genome phylogenetic trees cannot tell the full story of recombinant viral evolution.

Blasting the novel sequence region against all non-viral sequences (to pick up vector technology) again results in pShuttle-SN (no surprise) but now this time is also picked up a recombinant coronavirus clone Bat-SRBD spike glycoprotein gene from UNC, USA, (Genbank entry) and other synthetic constructs.

2019-nCoV coronavirus
As I published earlier, before anyone points fingers at the Chinese, note that recombinant viruses have been in play in laboratories all across the world in many nations.

The overlap occurs at the 3′ end of the novel region (search restricted from 21600-22350 bp in the query) 2019-nCoV sequence originally blasted against the other coronavirus CDS. It could arguably merely be that I selected too large a region; I chose the region visually to include the fully potentially inserted sequence including any homologous vector elements at the 5′ or 3′ end.

It is worth pointing out that due to the length of overlap, the sequence strength is considered moderately strong: highly significant E-value, high %identity, but short sequence length. These findings cannot be considered strong validation for obvious reasons: produced by the same analyst, using (part) of the same data. Spike proteins determine receptor binding for entry into cells, and 2019-nCoV appears to, like some bat species SARS coronavirus, target ACE2 receptors.1

For those tracking closely, I confirmed that the novel inserted sequence in the large alignment above is the same as the novel sequence I reported a few days ago. The sequence of interest is here.


1. Hou et al., 2010. Angiotensin-converting enzyme 2 (ACE2) proteins of different bat species confer variable susceptibility to SARS-CoV entry Arch Virol 155:1563-1569

2019-nCoV coronavirus
2019-nCoV coronavirus
These results do show, however, that the novel sequence is not likely present in other coronaviruses.

Thus, it still seems prudent that this inserted sequence in 2019-nCoV become the focus on urgent research, and that laboratory sources be included in the search for the origins of 2019-nCoV and potential targets for treatments and expected pathophysiology in patients infected with 2019-nCoV.

I am grateful to Dr. Wathelet for this inquiries and requests for additional clarification.