Systems & Intrinsic Disorder: MERS-CoV's "Hard Shell" Is Key To Understanding Its Epidemiology

Since 2012 our take on MERS is that it is either wide spread (via Hajj) and of little risk, or that its not very contagious and again of little risk. Since that time, enough epidemiological information has come forth for us to deduce from a systems analysis that MERS-CoV has adapted itself to thrive in a very specific anthropogenic environment and outside of that (or similar) environment MERS-CoV won't sustain deadly pandemic reproduction.

Our hypothesis is that MERS-CoV's specific adaptation is the development of a "Hard Shell". That hardened shell allows MERS-CoV to survive in desert fecal aerosols, while also allowing it to survive as a wet fecal fomite or aerosol, even after Islamic cleansing rituals have taken place.

Based on our analysis, a search of relevant literature showed that others have come to a similar conclusion but a via a completely different path. (see sources below) Their path was based on determining the amount of 'flexibility' in MERS-CoV's inner and outer shells via Protein Intrinsic Disorder Prediction. The conclusion was that of all the Corona viruses modeled, MERS-CoV showed the lowest disorder /  hardest shell, and thusly was likely fecally transmitted .

Frankly, this finding should not be surprising since other animal Coronaviruses like SARS and Feline-CoV have been documented to spread via aerosolized wet feces and aerosol dry fomite dissemination. Where as, Human cold causing Cornoaviruses are believed to be spread via sneezing and coughing.

What it means in the Desert:

The dry environmental spread of MERS-CoV is likely from a desert dwelling animal that produces very dry dung. The Camel is a prime example, its fresh dung is immediately ready for burning, and is often collected for that purpose. Its safe to assume that people down wind of Camel (or Human) desert deposited excretia are at risk if Human disease producing MERS-CoV is present . For MERS to survive this kind of dust blown dehydrated environment it likely must have a hard shell.

What it means in the Hospital:

The other unusual aspect of MERS infection is that chain transmission has occurred only in hospitals in the Kingdom of Saudi Arabia [KSA]. Given the wealth, and Islamic piousness observed in KSA, this means that MERS-CoV must transmit in a western medical environment which strictly follows Islamic cleansing / palliative care requirements.

In short, KSA's wealth allows more health care workers per patient; a lot more health care worker exposure to fecal matter via close physical patient contact/care; and significant health care worker inter-exposure via common restrooms in which no toilet paper is used to block fecal hand contact, but instead soapy hands are relied for posterior cleanliness. For MERS to survive in this environment, it must have some resistance to soapy water aerosolization or fomite deposition degradation; again this points to a hard shell.

What it means outside of Saudi Arabia:

Given the lack of deadly MERS chain transmission outside of KSA, and our previous stated conclusions; it appears that lethal MERS transmission requires a minimum exposure dose, one which MERS has adapted to allow KSA hospital care to deliver. Outside of a wealthy discrete healthcare environment, similar dose exposures in a distributed environment might be expected to occur in poor, high population density areas with similar cultural / religious practices. This epidemiological analytical transformation is analogous to a MERS smart bomb on discrete target vs a cluster bomb on an area target. One might also expect chain transmission to occur in western nursing homes.

What it means for HAJJ:

HAJJ has not yet supported deadly MERS chain transmission, but that does not rule out that it will.

Quick Conjectures:

#1 One possibility is that Camel Coronavirus in Humans is to MERS, as Feline Coronavirus[FCoV] in Cats is to Feline Infectious Peritonitis [FIP]. CATS living in high density populations often have FCoV, but only in a small percentage of cats does that infection internally mutate into the disease manifesting version which causes FIP. The disease causing version is not believed to be transmittable to other cats. Since MERS is transmissible, a worst case reinforcing scenario would be a human MERS patient infecting a Camel with "human MERS".

#2 Camel herders are immune to MERS akin to the way in which Milk Maids were immune to SmallPox.

#3 If the in country dwell time for HAJJ pilgrims remains below the median time for symptom onset from exposure, the odds are an outbreak inside of Saudi Arabia is self limiting.

#4 The risk of a massive MERS outbreak at Hajj increases as a function of KSA's gross domestic product per (transient population) capita decreases.

Sources:

Prediction of Intrinsic Disorder in MERS-CoV/HCoV-EMC Supports a High Oral-Fecal Transmission

Bedouin Camel Coprophagia Dysentery Cure A Pathway For MERS Infection

MERS Likely Spread Via Islamic Palliative Healthcare

MERS-CoV Infection Via Diarrhea & Eastern Toilet Habits

Feline Infectious Peritonitis

How cats become infected with feline coronavirus, the virus which causes FIP

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Complex Systems: Origin of Virulence; Chaos, & Radioactive Black Dirt

  We don't own this video, we uploaded it for YouTube's friendly controls, and because it actually features a Systems thinker working in a field of myopic bean counters, most of whom have no understanding under what boundary conditions their methods / tools produce garbage.

If your only interest is in Radiation, and why contaminated soils turn black skip to 29:28
If you want info on how black mushrooms may prevent radiation sickness skip to 34:54
If your interest is chaos and virulence skip to 37:50
If you want to understand why there are few systems thinkers in Biology and related Sciences watch the entire video.
If you want to understand why much of peer reviewed Quazi science is a scam, skip to 43:21
We use the term quazi-science because the methods used are based on self referential mathematical inference.

There are a some weakness in the presentation, the most glaring of which involves passive global warming acceptance.

Here are the video details from NIH
:
Category: Joseph J. Kinyoun
Runtime: 00:56:48
Description: The worlds inside and outside our bodies teem with microorganisms, but most don’t make us sick. Fungi in particular seem to leave mammals alone. Of the 1.5 million known fungal species, only a dozen or so are relatively common human pathogens, while insects and plants are frequent fungal targets. Why the difference? Arturo Casadevall, M.D., Ph.D., will address that question—and the intriguing possibility that the demise of dinosaurs and the rise of mammals were linked by differing susceptibility to fungal diseases—in the 2013 Joseph J. Kinyoun Memorial Lecture.

Casadevall is Professor and Chair of the Department of Microbiology and Immunology at Albert Einstein College of Medicine of Yeshiva University in New York. His research centers on the questions of how microbes cause disease and how hosts, such as humans, defend themselves. To explore this dynamic relationship, Casadevall and colleagues have long examined Cryptococcus neoformans, a common fungus that is harmless to healthy people but can cause serious disease, including lung infections and fungal meningitis, in immune-compromised people such as those with HIV/AIDS. Many of the laboratory’s projects seek to understand how hosts defend against C. neoformans and how the organism’s virulence contributes to disease.

Casadevall received doctoral and medical degrees from New York University and completed an internship and residency in internal medicine at Bellevue Hospital in New York City. He is the author of more than 570 papers and currently serves as Editor-in-Chief of the online, open-access journal mBio. Casadevall is a fellow of the American Association for the Advancement of Science, serves on the National Science Advisory Board for Biosecurity, and co-chairs the NIAID Board of Scientific Counselors.

NIAID established the Kinyoun Lecture series in 1979 to honor Dr. Joseph J. Kinyoun, who in 1887 founded the Laboratory of Hygiene, forerunner of NIH, which launched a new era of scientific study of infectious diseases.

For more information go to http://www.niaid.nih.gov/news/events/meetings/kinyounSeries/Pages/2013KinyounLecture.aspx
Author: Arturo Casadevall, M.D., Ph.D., Albert Einstein College of Medicine of Yeshiva University in New York
Download: Download Video How to download a Videocast
Caption Text: Download Caption File
CIT Live ID: 13248
Permanent link: http://videocast.nih.gov/launch.asp?18211

Beautiful Baby Girl Picking and Eating FUKUSHIMA Blueberries

Even in the heart of the darkness people refuse to see the high speed photons.



UPDATE:

The video has now been made "Private", in the interests of "fair use" (commentary, criticism, news reporting, research, teaching, library archiving and scholarship) I have updated this report with a few screen shots of the video:

The original information and translations may be found at the end of the post.

Video description from the uploader niidamasugata:

We went to blueberry picking in Niwasaka, Fukushima-city.
Part of Fukushima-prefecture is subject to the government control.
This area is not restricted area.
Radio active material was not detected in these berries.
Farmers in Fukusima-prefecture were hit by rumors.
Even if radio active material was not detected, consumer does not buy any foods made / produced in Fukushima.
It's unseasonable!
Of course it's your decision call us stupid parent who does not protect child from radioactivity.
They are just words, from far away from Fukushima


a follow-on comment from the uploader niidamasugata:(Translated by Google)

• The explanation for the lack of English skills and their written in Japanese like it I is misunderstood - The. It had been completely polluted 'Place is a neighborhood has confirmed , Has confirmed that there were also contaminated crops were harvested. I believe the word means no foreign • non Fukushima Land, people living in Tokyo, for example, all-risk coverage and incite the media, particularly believe in Fukushima - That is to say. After decades • my own children "or 逃Genakatta Why?" And blame Has been recognized that it may be. The purpose of this video posted, it was because the sight of a girl ask a friend abroad . Some people can not see the video was quite a provocative picture is observed - Or. However, it is disappointing for me. So video is going to be removed soon. Please let me say the last one. My friend calls and emails every day from friends who live in other regions, "or What are you Fukushima, "" flee as soon as possible "is attacked, and mental illness 冒 - I now. I think the advice out of kindness, acts such Fukushima I would like to know given the fact that mental distress.


Original Japanese:

• 自分の英語力と説明不足の為に、誤解されてる様なので日本語で書¬きます。 ・自分の住む地域が全く汚染されてしまった事は認識していますし¬、収穫された　農産物も汚染されたものがある事も認識しています。 ・外国人の言葉だから信じないという事もありません、福島以外の¬地域、例えば　東京に住む人達、特にマスコミが福島＝全て危険と煽る報道は信じ¬ないという　事です。 ・何十年後、私は自分の子供達に「何故逃げなかったか？」と責め-られるかも　しれないという事も認識しています。 この動画投稿の目的は、海外の友人に娘の姿を見てもらう為でした¬。 見る人によってはこの動画がかなり挑発的な映像であった事は認め¬ます。 しかし、それは私の本意ではありません。 よって近日中に動画は削除するつもりです。 最後に一つ言わせてください。 私の友人は他地域に住む友人から毎日のように電話やメールで「ま¬だ福島に いるのか」「一刻も早く逃げなさい」と責められ、精神的な病に冒-されてしまいました。 親切心からのアドバイスだと思いますが、そういった行為が福島県¬民に精神的な 苦痛を与えているという事実も知って頂きたいと思います。

Little Lord Fauntleroy is back in the pink!

Dr. Keith Ablow has written an amazing article over at Fox News, about gender boundaries.  He wrote in response to a J Crew ad showing a mother painting her little boy's toenails pink.

To the surprise of no one, (n=1)^1000 crowd hit their typewriters full force in the comments sections, to decry any attempt to establish and celebrate differences in the sexes.   While most agreed that forces of nature could not be denied, they were perfectly willing to try denial until nature became insurmountable.

So much for celebrating diversity.

The hundreds of commenters who wrote their n=1 hypotheses followed an identical template.  'My mother / sister / aunt / grandmother put makeup / nail polish / dresses / long curls on me and I turned out okay, so what's the big deal?'

Who's right?  The army of Fauntleroy enthusiasts, or the creepy looking friend of Glenn Beck?

"Who" you ask, "is Fauntleroy?"  Before I answer that, I just want to say in fairness (since I liked his article), that the good doctor looks less creepy in other photos.  Just the Fox one is odd.

So.  Little Lord Fauntleroy is a fictional character created by Frances Hodges Burnett of Secret Garden fame.  Fauntleroy was the anti-child, ridiculed, mocked and despised by real children; beloved, uplifted and extolled by parents.

A lad of 5 or 6, he lived with his beloved mother whom he called "Dearest"; waiting lovingly on her with hand and foot.  But most importantly, Fauntleroy was always immaculately garbed in suits and skirts, white kilts and black velvets, all crowned with 'shiny golden love locks that curled about his shoulders'.  As boys go, Faunt was an effeminate fop, who all mothers yearned after.  He was gender neutralized - old school.

In that day and age, foppishness and effeminacy was called "dressing your boy up as a young lord", and as it always has been throughout history, aspiring to wealth and aristocracy meant the adoption of effeminate softness.

Smooth slippery fabrics, powdered wigs, makeup.  Louis XIV's standards of opulent decay are historically cured only when lopped off at the neck.

That, is the point Dr. Ablow is trying to make.

The Faunts' mom didn't promote effeminacy by saying "it doesn't matter to me if he wants to like girls or boys or sheep when he grows up, or has certain body parts amputated like the pet dog.  I'm big enough to love whatever he turns into".  Loudly expansive toleration of the ostentatious  is a modern point of Munchhausen pride.

But pride of the ostentatious, whatever the trappings, has been a constant theme throughout history.   Ostentatiousness promises money, power and influence and attracts all who love those things.

Idle hands, ill gotten gains and the love of money prescribe national failure.

Though Fauntleroy single-handedly popularized the lace cravat in size 5T for a time, America was still young and industrious and in theory at least, opposed to rank and aristocracy.  Trends soon drifted toward a hard bitten masculine fashon, but without the communist abhorrence for wealth.

So is the J Crew mama just a silly woman putting her daughter-yearnings on a good natured, tolerant son?  Or is she consciously promoting the effeminacy that represents class and aristocracy, afforded by wealth and idleness?

I suggest it is in fact irrelevant what Jenna Lyons personal motives were.  What is relevant is that the photo and caption were published by a company trying to sell things.  And that company, which depends on the patronage of the wealthy for survival, is appealing through abject effeminacy. 

That answers the question, don't you think?

Heed Dr. Ablow.  If we are lucky, the worse that will happen is our wealth bubble will pop.  If we are not, well, I hope this time we get some chain mail woven into those lace cravats.

The Cookitarians hit the big time

It wasn't that long ago that I wrote a post about Grainitarians, and mentioned the "Cookitarian" philosophy in passing.

Now, they're making headlines. Headlines at Medical News Today at least.

Richard Wrangham, the father of Cookitarianism has published a book "Catching Fire: How Cooking Made Us Human".

The article states

Drawing on a wide body of research, Wrangham makes the case that cooking makes eating faster and easier, and wrings more caloric benefit from food.

This is my favorite part:

By freeing humans from having to spend half the day chewing tough raw food -- as most of our primate relatives do -- cooking allowed early humans to devote themselves to more productive activities, ultimately allowing the development of tools, agriculture, and social networks.

So this raises two questions.

One, our dogs and cats have subsisted on our cooked food for at the better part of a hundred years now. When can we expect them to stop wasting all their non-masticating time laying around the house, and do something productive for the family?

And two, what does this mean for the raw food movement? Ok, that's not really a question. I think we already know the raw food movement accepts the chains - Raw Food: "It’s not a diet. It’s a way of Life."

Who killed the Neanderthals?

You. And you. And you over there. We all did!

At least, our great(^nth) grandparents did.

Ha. Take that Neanderthals.

And take that, gorillas that use sign language.

The similarities between animals and humans are constantly used as arguments for why we shouldn't eat them, or use them for our (devilish) purposes. Ever since Peter Singer published the nauseating Animal Liberation bromide

"If possessing a higher degree of intelligence does not entitle one human to use another for his own ends, how can it entitle humans to exploit nonhumans for the same purpose?"

peta-tics have crapped themselves trying to prove that animals are equally intelligent to humans, as though making the Singer argument a de facto point would make it a fact.

But in fact, if we casually consumed our closest homanid, the Neanderthal, the much stronger argument is that our own advancement depends on the consumption of the "competition".

Where are the Grainitarians?

It is the primary unanswered question of meat-free diets. We've all heard the arguments, about how we are soooo like the herbivores, and soooo not like the carnivores, therefore we should eat plant based foods.

The problem is, most of these herbivores eat grass. Not grain. These herbivores we are supposed to be so similar to, get into lots of trouble when their diet becomes heavy with corn, wheat, oats etc.

PBS Frontline hosted an interview with Michael Pollan that revealed what happens to our cousins the herbivores when they eat grain.

Cows are not evolved to digest corn. It creates all sorts of problems for them. The rumen is designed for grass. And corn is just too rich, too starchy. So as soon as you introduce corn, the animal is liable to get sick.

It creates a whole [host] of changes to the animal.

You start giving them antibiotics, because as soon as you give them corn, you've disturbed their digestion, and they're apt to get sick, so you then have to give them drugs. That's how you get in this whole cycle of drugs and meat. By feeding them what they're not equipped to eat well, we then go down this path of technological fixes, and the first is the antibiotics. Once they start eating the [corn], they're more vulnerable. They're stressed, so they're more vulnerable to all the different diseases cows get. But specifically they get bloat, which is just a horrible thing to happen. They stop ruminating.

So you put in the corn, and this layer of slime forms over the rumen. You've got to picture the rumen. It's a 45-gallon fermentation tank. It's essentially fermenting the grass. Suddenly your slime forms and the gas can't escape, and the rumen just expands like a balloon. It's pressing against the lungs and the heart, and if nothing is done, the animal suffocates.

So what is done is, if you catch it in time, you stick a hose down the esophagus and you release the gas and maybe give the animal some hay or grass, and it's a lot healthier. But it's one of the things that happens to cows on corn. ...

Slime. Eeewww. I've seen hams with horror movie quality slime on them (ok that's another story but still gross.) Poor cows. How cruel is it to force the poor herbivores we are sooo much like to be grainitarians. Is it more cruel than eating them?

But we don't eat grass or hay. So maybe the ruminent herbivores are not the ones we are so like after all.

I know! It's apes. They are vegetarian (or are they) and genetically very like us. They must be the herbivores we are so very like.

Well, here is dedicated carniphobe McDougall on our ape cousins.

The diets of great apes, like those of chimpanzees, our closest relative, are nearly pure vegetarian in composition; consisting largely of fruits, and in the dry seasons when fruit is scarce, they eat tree seeds, flowers, soft pith, and bark; with termites and small mammals making a very small contribution all year long. Chimpanzees eat very little starch.

Dr. McDougall, you see, thinks everything can be cured by a vegetarian diet. However, he will only hold this claim if it is a starch-based vegetarian diet. So if even says we are not like the chimpanzee, then they must not be the herbivore our vegetarian pre-disposed systems are modeled after.

Additionally, chimps have been observed eating meat in the wild. Real meat, like bush pigs, not just the better known termite fetishes.

What does that leave?

Vermin. Mice, rats, gerbils etc. Rodents.

Are we like rodents? (I don't think that is quite what the 'we're all vegetarians by design' crowd has in mind, but for the sake of full disclosure, we'll investigate.)

Small mammal nutrition tells us that rabbits eat green leafy things, they are strict herbivores and grains can lead to gastrointestinal disease (ok, sounds like cows). Yes, I know rabbits aren't rodents, to most people anyway. My dog I'm not so sure about.

Guinea pigs and chinchillas are like rabbits.

The real rodents, the climb on the chair screaming 'There's a Rodent' rodents, are a little different. They eat everything. Plants and meat and of course they are notorious for eating grain. But what happens to the mouse and rat when it eats only vegetarian foods? Well, how does cannibalism sound? Okay, what about mouse-ablism? Better? Ratablism?

The Ratablism link is a FAQ from a rat breeder. Not hard science, but breeders can make some very valid observations.

Belief: Feeding meat will make rat vicious.

Basis/Reality: WRONG. Meat products are a necessary part of a rats diet. Rats are omnivores. That doesn't mean they CAN eat both meat and vegetable products, it means they MUST eat a varied diet that contains both in order to be healthy. There is absolutely no evidence that a diet rich with meat makes rats or any other animal vicious. There is evidence to the contrary! If rats are denied meat products such as a kibble, rodent block, or a little egg or chicken in their diet, they will and have had to turn elsewhere for the nutrients they need. This may involve preying on mice (or trying their best to!) nearby or catching bugs--whatever it takes. The rare instances where rats have eaten the flesh of other rats or killed other animals often take place when the rats have an incomplete diet. (Especially in pet stores where they are fed only grains and kept in close proximity to other rodents they can hunt.) BTW, I have among the most gentle rats I've ever known, and they regularly get leftovers including bones and meat--in addition to their dry diet which includes kibble. Only a despirate or starving animal is a "vicious" animal...

So where does that leave us?

One idea is that we are just unique. We are, 'Cookitarians'. Meaning it doesn't matter what our food of choice, as long as we cook it.

Dr. Richard Wrangham, a Harvard professor of anthropology, attempts to explain why we are alive today and have not become extinct because we are so poorly designed. He thinks that humans survived because they learned to cook.

Okay. Maybe. I think the evidence comes down most strongly on the side of the carnivore. The Eskimos (Inuit) pretty much disproved the cooking philosophy. Archeologists are routing any concept of agricultural societies being healthier than hunter-gatherers.

And then there are the socialogical implications, that would be really fun to post about. For example, what happens when a agricultural based society begins to enjoy a higher fertility rate than the hunter gatherers? Oh yeah, mortality is higher, so no prob. BUT. What if we fix the mortality problems caused by the agriculture with our superior technology developed by our cooked food enhanced brains? Mortality Redux.

Hmmm. 6 Billion strong. Someday we'll figure it out.

In the meantime, I still want to know. Which obligate vegetarian mammals are we designed like again?

Roll Over Darwin.

You're stifling learning. Evolutionary biologist Stuart Newman says

people are concerned if they open the door to non-Darwinian mechanisms, they will let creationists slip through the door as well.

What non-Darwinian mechanisms could he be talking about?

Well, says Newman, "self-organization represents a challenge to the Darwinian theories of natural selection."

Darwinian orthodoxy, you see, says everything is incremental.

Wikipedia (where most people seem to get their understanding of evolution) says

While the fossils cannot undoubtedly prove common descent, they are highly suggestive of it if they show two patterns:[1]

* older forms are simpler than newer forms;
* the number of species increases with time.

The fossil record certainly meets the first criterion. Among the earliest mammalian fossils, there are no specialized mammals like whales, but we do find fossils of whale-like terrestrial mammals that possessed underdeveloped legs. The second criterion poses a sort of impasse between evolutionary scientists who claim their findings to be incomplete yet compelling and creationists who bemoan them as severely lacking.

These gaps in the fossil record are a problem for the theory of darwinian evolution.

Punctuated Equilibrium is another explanation for the fossil gaps. It fell out of favor for a while, but now the top evolutionary scholars are re-assessing its potential. Like self-organization, punctuated equilibrium creates a problem for the darwin religious sect. You know who they are, they will ask you if you "believe in evolution", or condemn you if you don't "believe in evolution".

Farmers who don't believe in evolution. Oy vay.

End of discussion. - Heather Houlahan

Darwin proposed natural selection as the mechanism for 'Common Descent'. Natural selection has been observed, but is yet to be substantiated as the driving force of species jumps.

When most people talk about evolution today, they really mean "natural selection". When they ask you if you believe in evolution, they are asking you an impossible question. Of course you don't have to believe in natural selection, it has been observed. And since natural selection isn't the only (or even perhaps most critical) force in generating separate species, no one should sign up to believing in 'Darwinian Evolution'. But if you don't? Oy vey.

Epigenetics has thrown another wrench into the previous understandings of natural selection.

And for the final word, the entertaining Fred Reed asks questions that have yet to be answered...

If the faithful of evolution spent as much time examining their theory as they do defending it, they might prove to be right, or partly right, or discover all manner of interesting things heretofore unsuspected.

At any rate, the idea is that slight selective pressure (operational definition, please? Units?) over enough time produces major changes. The idea is appealingly plausible. But, for example:

(1) A fair number of people are deathly allergic to bee stings, going into anaphylactic shock and dying. In any but a protected urban setting, children are virtually certain to be stung many times before reaching puberty. Assured death before reproduction would seem a robust variety of selective pressure.

Yet the allergic haven’t been eliminated from the population. Why is it that miniscule, unobserved mutations over vast stretches of time can produce major changes, while an extraordinarily powerful, observable selective pressure doesn’t? The same reasoning applies to a long list of genetic diseases that kill children before they reach adulthood. (Yes, I too can imagine plausible explanations. Plausibility isn’t evidence.)

(5) If intelligence promotes survival, why did it appear so late? If it doesn’t promote survival, why did it appear at all?

(8) So much of evolution contradicts other parts. Sparrows evolved drab and brown so that predators won’t see them. Cockatoos and guacamayas are gaudy as casinos in Las Vegas so they can find each other and mate. But…but….

So get over Darwin already, and let people question evolution. Maybe we'll actually learn something.