Facts, not Fantasy

Thursday, March 29, 2012

Evolution and Vaccination - A destruction of an anti-vaccine argument

It's no secret that a lot of the anti-vaccine movement exists due to the ignorance of parents who need to make decisions with their child's healthcare. Anti-Vaccine portrays themselves as scientists when they are not often using acronyms and official sounding degrees and lab coats to make themselves seem like they are professionals.

They work by creating unreasonable doubt and by portraying their qualifications as equal to a medic when in reality they generally follow incredibly outdated medical practices and ideas that are laughably out dated in a science that is moving at a pretty hefty pace. They lie and portray deadly diseases as "harmless" and easily controlled by nutrition, vitamins and magic water.

They show a complete lack of understanding of statistics, probability and actual terminology and appeal to ideas like "souls", "harmony", "balance" and "energy". Words which mean very little in terms of the biochemical machine that is your body and are even more vague when one asks them to describe a medical condition.

Today we deal with Vactruth's article by Bunny St. Marie on Vaccine Resistant Pathogens. And it is basically a collection of incredibly daft ideas that need to be dismantled comprehensively lest I be accused of quote mining and taking ideas out of context.

You would probably laugh at the absurdity of it—dangerous mutant invaders, seemingly by stealth, plotting a massive attack against the human race.
But, what if you discovered those mutants would be invisible to the naked eye? Would you still have a hard time believing such a story? Believe it or not, many scientists have begun warning us about that exact scenario, with one exception: Microscopic viruses and bacteria are actually playing the roles of the mutants.

Evil Mutants!

Real Mutants
Medically speaking we are all mutants. Every single goddamn one of us is a mutant and has at some point had a mutation. Using such language in a medical explanation is fraught with peril since we are confusing what the word mutant means.

A mutant is any organism with a genetic variation from the fused original genome created at fertilisation. It can either be expressed as a local mutation (eg. Cancer) or a silent mutation (eg. Most People will probably have one cell with a silent mutation) or a germ line mutation (your kids will express a mutation.)

The best example of a mutant is the good olde humble wheat plant.

It's a single and simple mutation that made this plant one of the earliest domesticated crops and it's a mutation that's common to all crop plants. Tame wheat has a mutation that prevents it from spreading it's seeds. It does not shed it's seeds and they ripen on the plant.

Now normally this is a massive disadvantage except, if there is a species out there that actively promotes this mutation. Spreading it across the world and actively killing individuals of this species that do not show the mutation. Now this mutation would be an advantage. Which is why there are more tame wheat plants out there than wild wheat. We actively protect wheat from predators, disease and spread the seeds hence the mutation is common.

Not so scary now right? The usage of mutant is to scare the fuck out of people. It's a calculated accusation made by Bunny to scare people into thinking of these mutants as the twisted warped individuals because she is trying to imply that vaccination somehow causes mutation. And she does this with the grace and panache of a blancmange.

I like my mutants like I like my scotch, 13 - 18 years old, green and ninja.

The simple fact is this: You have been advised by your doctor to rely on vaccines as a defense against microscopic invaders.

We actually encourage a variety of defences against infection ranging from "Washing your hands" to "Vaccination" to "Pasteurisation" to "Cooking Your Goddamn Turkey"

But what happens when a pathogen manages to outsmart such pharmaceutical measures? We may be finding out sooner than expected. Here’s why.
Pathogens such as bacteria and viruses cannot outsmart anything because they don't have brains. They are evolving. The mechanism of their evolution is random and driven by their massive reproduction rates. They aren't trying to "outsmart medical technology" they are doing so to survive. If they do not evolve they die. Smallpox is an example of a pathogen that didn't evolve. Polio is an example of one that probably won't evolve by the time we make it extinct. The nature of these viruses was to affect only humans and that specificity was both the reason for their success and the reason for why vaccination is so succesful against them. 

Then there were the recent measles outbreaks occurring in both the U.S.A. and Canada. Sporadic outbreaks of meningitis also have been reported around the globe over the last couple years. Just this year, an outbreak of meningitis was reported in the States. [1]
The recent measles outbreak in the USA is mainly seen in unvaccinated groups of people as the vaccination rate of both countries had dropped quite heftily due to the efforts of anti-vaccine and autism activists who believe in the MMR link. This produced a fairly hefty fall in vaccination rates allowing for the reoccurence of measles.

A quick check shows that between 2007 to 2008 in the Israeli Measles outbreak majority affected were orthodox and hassidic jews who do not vaccinate. France's low measles vaccination rate resulted in roughly 7000 cases in the first three months of 2011.

And lest we forget. Measles in the DRC has killed 1145 children due to the low vaccination and famine conditions but I am sure Bunny will blame the famine more than the vaccination rate and indeed claim that it's a perfectly harmless disease (If you are lucky enough to be born in the first world where fancy medicine prevents you from dying.)

And the most telling statistic is that in 2011 the CDC stated that it had 118 cases. Of 118 cases, 105 were not vaccinated. (89%). The US outbreak is actually rather small since the anti-vaccination and the fear of MMR isn't as hefty as seen in the UK where there were are roughly a 1100 cases a year and rising due to the lack of vaccination due to anti-vaccine fear mongers. Every single case, more people who were unvaccinated were affected than those who were vaccinated.

And this is without her first source which is from here. The vaccine we give is for pneumococcus (Streptococcus Pneumoniae) which can cause meningitis. The outbreak is for meningococcus (Neisseria Meningitidis). They are entirely different diseases caused by entirely different bacteria.

The issue that a lot of people have is the assumption that all bacteria are the same. The difference between these two bacteria is enormous. As wide an evolutionary gap as ant and human. They both belong to the kingdom of bacteria but diverge at the phylum level at a fundemental scale. Pneumococcus is a gram positive bacteria while Meningococcus is a gram negative bacteria. It may sound petty and small but it's a massive and monsterous difference to anyone who has read about microbiology. To mistake the two is not a fundemental error when dealing on organisms on this scale. It is idiocy.


These were both stained with the same staining method and the difference is clear as day since streptococcus forms violet chains of cocci while neisseria does not appearing as pink binary forms. But clearly Bunny didn't check any of this before making her fallacious claim.

The meningococcus vaccine is a recent invention. It is being rolled out as we speak. We do really want a vaccine against this horrific disease and it's recent approval still means it hasn't been widely taken up and it isn't a compulsary vaccine yet.

As a parent, you are told if your children are vaccinated they are ‘protected’; yet many of the outbreaks have occurred in fully immunized populations. So what’s going on? Some argue outbreaks may have originated from a foreign traveler or possibly from children whose parents chose to exempt them from vaccines. While others feel a far more worrying mechanism is at work. One possibility being common pathogens have mutated and not only become resistant to vaccines, but also potentially more deadly.
No. Many of these outbreaks occured in populations where vaccination rates are shrinking and where many people have lapsed their vaccines or avoided boosters. And bear in mind the UK's "full vaccinated" rate of measles is the same as the DRC's mortality rate from measles and you quickly realise how effective vaccination really is. What Bunny has done is tried to portray the American Public as heavily vaccinated while failing to mention that most cases as reported by the CDC (which no doubt she refuses to trust) are from unvaccinated groups or from diseases that people haven't been vaccinated for.

And a vaccine is not 100%. No one said it was. Nothing is 100%.. You can still catch a disease that you have been vaccinated for, it's just that it is a lot more unlikely than before.

It's the equivalent of wearing bullet proof armour in a gun battle. Sure you may not get hit but why take the chance. It is the equivalent of not wearing a seatbelt in a car. Sure you may not get into an accident but why take the chance. You may not get measles but why risk it by not vaccinating. And the statistics were clear on this. At one point everyone got the measles. Not vaccinating will result in a re-establishment of rates. This much is clear in the UK where the number of cases has risen courtesy of the MMR/Autism link lobby and their arch-quack, Andrew Wakefield.

Added to which pertussis is almost unheard of in children and mainly affects older adults and infants as pertussis immunity wears off rapidly even from natural infection (at the same rate as the vaccine) and adults don't keep up with booster shots.

For example, a particular study published in 2010 mentions the rising increase of whooping cough cases may be caused in part to the use of acellular pertussis vaccines resulting in the adaptation of circulating pertussis strains. [2]
Here Bunny shows a phenomenal ignorance of what the scientific paper is about. In her mind the vaccine somehow mutates the bacteria.

What the study shows is the change in allele frequency in pertussis strains caused by vaccination. There are local antigenic variations and the pertussis vaccine that is currently used is the acellular vaccine (the Whole Cell Vaccine causes a bigger reaction but with greater side effects such as fever as the body recognises the whole bacteria and activates a proper immune response). The acellular vaccine has a lower effectiveness rate (around 75% to 85%) but is preferred due to it's safety profile.

Now what occured here is that various antigens of the most common strains were used in the vaccine to protect against them. Thus leaving the least common strains partially protected or with no protection at all. This results in a prevention of infection by the most common strains which quickly reduce while the least common ones are not affected as much until we reach the situation where the previous common strains have become rarer. As seen in the case wher MT70's incidence drops below MT10 in the UK due to MT70's usage in the vaccine.

What Bunny is demonstrating is a phenomenal ignorance of how evolution works. You don't evolve to meet a threat. You evolve over generations rather  than as a single individual and if you can survive a change of environment you survive, if you cannot you go extinct. What we see here is allele frequency alteration due to the arrival of the vaccine and the reduction in possible prey for the common strain.

Another study led by Dr. Frits Mooi suggests whooping cough vaccines are becoming less effective due to certain strains of pertussis adapting, and that these emerging new strains are likely more virulent. Indeed, the epidemiologic data found an association between these new strains and an increased infant mortality rate. [3]
This study into virulence is quite interesting. Basically it boils down to comparing two of the common strains of pertussis and some astute observations. It basically looks at the allele frequency changes of Pertussis Toxin 1 vs Pertussis Toxin 3.

Now basically Pertussis Toxin is not normally excreted by the bacteria. There is a disadvantage to wanton usage possibly a negative metabolic effect making toxin 3 rarer pre-vaccine. The paper mentions this. However in a host they both produce the toxin. However after vaccination the incidence of pertussis toxin 1 went down while toxin 3 went up. The net number of cases fell but there were still incidents.

The paper points out that those with Toxin 3 are more virulent than Toxin 1. Not virulent enough to affect a fully healthy adult with a vaccine but sufficient to create a latent or silent infection. And then he points out what the cause of the increased rate of infection is.

Dr. Mooi points out that the main reason for this is PTx 3 has a immunosuppresant effect and in order to overcome this increased virulence the body requires a longer period of time to produce the necessary antibodies allowing for the potential spread due to the increased efficacy of the toxin and the increased production. PTx 1's lower virulence means that it is much more easily killed off by the immune system. Dr. Mooi points out that the rise in PTx3 has three main causes.

Firstly, vaccine quality varies across the board. The quality of vaccine varies. He recommends that vaccine quality be improved as he noted that recently vaccinated children do not catch pertussis of either type. Their immune system responds heavily.

Secondly, the current vaccines do not produce antibodies against PTx3 and it's increased anti-immune effect. Addition of antigens from PTx3 and 1 would improve the vaccines.

Thirdly, adult vaccination is low and most adults are partially immunised resulting in longer response times and spread of PTx3 allele variants.

In short? Improve the Goddamn Vaccine and get adults boosters is this man's conclusion. Bunny's is Do Not Vaccinate At All. Fuck the half a million or so people a year the Pertussis vaccine saves. We shouldn't vaccinate at all! That way we can lose more children to the disease (roughly 80% of pertussis cases are in the 0-5 age group) and not have to worry about an increased virulence that means nothing to someone who is vaccinated. Never mind the fact that we can prevent this by improving vaccination.

What’s even more shocking is, according to the CDC, vaccinated children may actually be putting vulnerable loved ones at risk! A study published in 2000 found that vaccinated children are not only at risk for contracting pertussis after 4 to 5 years, but also may play a role in transmitting pertussis to vulnerable loved ones via asymptomatic (or silent) infection. [4]
The natural immunity for pertussis also wanes after 4 to 5 years. This is why we use booster shots. If you miss your boosters you can spread the disease. You don't gain a life long immunity from pertussis and we specifically mention that you do not gain such an immunity and require regular boosters in order to remain immune.

And it does point out that the reduced immunity in those who were vaccinated but missed boosters and recommends booster shots.

This isn’t an isolated problem with pertussis, either. Scientists also speculate about measles becoming resistant to vaccines.
This isn't a resistance to vaccines so much as a very minor latent infection rather than coughing so hard you break a rib. The problem is Bunny is embellishing the truth. Basically? Pertussis (a bacteria) has had an allele frequency shift to a more virulent allele PTx3 which provides better spread due to it's more toxic nature. This produces latent infections which spread in the short period of time it takes to mobilise an immune response and is mainly seen in vaccinated adults who lack the full vaccine and can be corrected via the introduction of the PTx3 antigen to the acellular vaccine and by keeping up regular booster shots even in adults to prevent the spread of this latent infection (sub-clinical) to infants.

Now here is the thing. A tiny experiment. Go get a bottle of coke and a white sheet of paper. Take a small mouthful. Now cough before you swallow. Aim it at a white sheet of paper. Notice the massive spray of coke on the white sheet.

Now imagine a disease spread by coughing. For example... Pertussis. Can anyone tell me why sub clinical pertussis with no cough is less likely to spread as much and as far than pertussis with a cough?

I am sure anyone can because we regularly deal with the Rhinovirus (cold). We know that it spreads via cough and via the air yet Bunny clearly thinks pertussis spread remains the same in such a situation.

A research team led by Dr. Claude Muller from the National Health Laboratory in Luxembourg has reported circulating strains of measles in Africa developing a significant level of resistance to the vaccines currently being used. [5]
This  article specifically says in the first few lines that the reason why resistant strains develops is poor vaccination. This is traditional anti-vaccine failure of written comprehension to go with their incredibly shoddy grasp of mathematics and their even worse grasp of science. The resistance is being caused by people like Bunny and her anti-vaccine movement.

Mainly her more deadly ilk like those alternative medicine practitioners in Africa who fight against local vaccination schemes. I must point out again the population of the Democratic Republic of the Congo and that of the UK are roughly the same at around 60 million and the UK has a rather high measles rate of around 1100 cases a year while the DRC with it's patch vaccination has one where the mortality alone is around 1000 cases a year with nearly 100,000 cases a year. This article only emphasises that the actual problem in Africa and indeed places like the UK is the anti-vaccine stance with particular emphasis on the uptake of the MMR vaccine.

But the evidence of morphing pathogens doesn’t end there. A new study has implicated evolving bacteria with the emergence of vaccine-resistant pneumococcus strains, the same bacteria responsible for causing pneumonia and meningitis infections. [6]
Actually... If you read the article it points out that this isn't an effect of the vaccine but a quirk of the bacteria which produces resistance to normal immune systems which is why you can repeatedly get infected from pneumococcus. This is a normal occurrence that the bacteria does even when there is no vaccination.This isn't even the same things as the other things. This is goddamn conjugation which is an entirely different process from the previous allele frequency changes. This is best explained via the fertility factor

And this specific issue has more to do with antibiotic immunity than vaccine resistance. And this is where Bunny plows on.
These troubling findings are very reminiscent of concerns that were raised after the over-prescribing of antibiotics. Scientists warned early on that over-use and failing to finish ones prescription could lead to bacterial resistance. [7]
No. These are nothing like the overprescription of antibiotics. Vaccines function by priming your immune system by mimicking an infection without the negative effect. Antibiotics work by affecting bacteria directly. And yes... failing to finish your prescription can lead to resistance but guess which group of people routinely tell people to quit taking antibiotics. It's certainly the group of people whose only qualification is that they managed to have a child and who assume that this landmark achievement allows them insight into the function of a human being that medical personnel do not.

Many years later, after the emergence of antibiotic resistant super-bugs like MRSA, both physicians and patients are now beginning to re-examine their approach to illness. Isn’t this similar to what is happening with vaccines? Consider this. Americans are the most vaccinated population in the world.
Actually. We can treat MRSA. Vancomycin, Ceftroline, linezolid, Daptomycin and Teicoplanin all show activity against MRSA and combination therapies show a lot of effect. In addition we have two new classes of antibiotics (over Linezolid) undergoing testing including a 5th generation cephalosporin, dalbavancin, iclaprim and neomonacin.

In addition we are looking into defensin - 1, cannabinoids, platensimycin and hydrogen peroxide dressings. Oh and we are also looking into phage therapy which is entering human trial stages and shows a 95% effectiveness rating.

So yeah. We do cure MRSA, it mainly harms people who are heavily sick (And no it's not hospital acquired. 85% of cases come from outside the hosptial) or have conditions like diabetes where their high blood sugar helps the bacteria grow.

The physician's re-examination of methodology due to MRSA is the use of multiple drugs to treat diseases and insisting that the patient finishes their antibiotics and not listen to anti-medical luddites. The argument being made is that we shouldn't have treated all those sore throats

Here’s the shocking reality: Children following the CDC’s recommended vaccine schedule will be injected with approximately 115 vaccine antigens, and that’s just within the first two years of life! [8]
Oh my! Antigens! 115 of them! An antigen is mainly made up of proteins and polysaccharides and their associations with each other and with lipids and nucleic acid. These are any such substance recognised by the body's immune system.

Within seconds after birth the baby's immune system is exposed to thousands of antigens in the bacteria of the world. Within an hour it has taken it's first feed and is exposed to millions of antigens in the milk of it's mother. The colostrum or first milk is laden with antibodies. These antibodies are however foreign to the baby and are recognised as such and destroyed. The baby begins to produce antibodies to these antibodies. There are millions of them in each feed the baby takes.

Every single surface, every single touch and every single breath of air contains bacteria and viruses that the baby is exposed to in the thousands at best and you really thing 115 antigens over 2 years means anything? Our immune system deals with assaults on it every second. A 115 antigens is nothing in one go. This is spread out over two years. And indeed this ignores all the repeat doses. It's a very naive approach to the issue and assumes that our body can only deal with one pathogen at a time. The way immune systems work particularly when vaccines are involved is that they process all the antigens simultaneously. Since there is no pathogen load to worry about there is no disease and the body is not strained. Basically? Macrophgages consume the antigens and present them to naive T-Cells which produce a variety of antigen equivalent antibodies. When a match is found the body shifts to producing that type of T-Cell which produces the necessary antibodies. Some of these T-Cells will remain after as memory cells which reactivate in infection and rapidly flood the system with antibodies if the antigen is detected. This isn't a conveyor belt.

Often in a real infection the infective bacteria will produce multiple antigens and the body will produce multiple antibodies to these. By Bunny's logic we wouldn't be able to cope with such an event.

In my opinion, this is an outrageous amount. Similar to over-prescribing antibiotics, it seems logical to step back and evaluate the consequences of such a thing as over-vaccination, and whether vaccination mandates are truly achieving the desired effects, or whether our children are slowly falling prey to newly emerging forms of historical illnesses.
In Bunny's Opinion comprehension is not a valid skill and neither is a basic grasp of science or mathematics. In her opinion as a lay person? In her opinion as someone who doesn't understand medicine at all? In her opinion as an individual who cannot explain how disease spreads? Or how immune systems work? Pray explain why should we take her opinion on the subject matter?

I wouldn't dream of telling NASA how to do their job. You would have to be a madman to ask me to fix your car, and I would have to be just as mad to claim that I could fix it. I know my limitations as a human being. It's why I would hire a plumber if my plumbing went wrong. It's why I prefer my house to be wired up by an electrician rather than some yahoo who claims to know what he is doing. And it's why taking medical advice to someone whose only qualification is that she has achieved something that most women of the planet will achieve is incredibly stupid.

It is people like her who are guilty of the foolishness of Speaking as a Mother. Her assumption is that being a parent grants you innate knowledge of human biology and medicine which entitles her to speak on the subject. And it irks me since she is surrounded by a coven of sycophants who basically feed her delusion that she can make healthcare decisions regarding her children without any grasp of the subject material. Actually, it's her children. For all I care she can believe in all the magic water and fairy wings she likes as long as it's just them she is screwing over. What irks me the most? Is that she is considered a voice of healthcare when she cannot tell the difference between a gram negative and gram positive bacteria and that she is encouraged to stand up and give medical advice that she will never ever be held responsible for. If you follow her advice and your child falls sick or dies then there is nothing you can do. She is not responsible for her stupidity. It's not her that pays the butcher's bill, it's people like your doctor who have to clean up her mess when things go wrong.

People like Bunny St. Marie only exists because vaccines eliminated major diseases making them a thing of the past. To her they are as legendary as dragons. Only diseases are real and still are around and they can come back if our vaccination rate drops sufficiently as we have seen across Europe. Her advice is functionally detrimental to your health. It is encouraging you to face down dragons by being a virgin, wrapping yourself up in meat and barbeque sauce while wearing wooden armour soaked in oil. 

Your survival rate goes up if you are two days from retirement.

1 comment:

  1. EXCELLENT post Avicenna! That's all I can really contribute to this tour de force!


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