Ebola Two Years On: Mistakes We Must Not Repeat

Ebola Two Years On: Mistakes We Must Not Repeat

WHEN THOMAS ERIC DUNCAN landed in the US and brought Ebola to Texas, infecting two nurses, one of whom was given then green light to board a plane even though she had been exposed, serious gaffs were made by CDC.  The nurses (in fact all health care workers) were given the wrong protection gear instructions from the CDC. Then-Director at the CDC Thomas Frieden was hauled in front of Congress, and skewered by the House Select Committee.  When Freiden testified to Congress that he would not be concerned about an outbreak occurring in the United States unless there was a mutation in this virus, and in his words, “there are none”, he was doing was CDC does best: he was putting policy before science.

There were actually 396 mutations in the virus compared to the strain isolated in 1995 from an outbreak in Zaire. I was actually analyzing them during the misleading hearings. The virus from 2014 was only 97.3% similar to the strain from Zaire, not “99.9999%” similar, as a CDC scientist incorrectly reported on a White House conference call in which scientists from the US were told to represent Ebola facts the way that the CDC wanted us to.  That was just before the White House asked the AP to stop reporting on suspected cases of Ebola in the US.  (All of these events, and the science of Ebola, are chronicled in “Ebola: An Evolving Story“.

One of those mutations, we now know, drove the infectivity of Ebola in an insidious manner.

The A82V Mutation

At the time, as Director of the Ebola Rapid Assay Consortium, I pressed, in every venue, in national meetings, and WHO conference calls, PCR tests might be missing infected individuals due to mutations, and that epidemiologists concerned about the rates of mutations were far off the mark [Read “Ebola Evolving: It’s Not the Rate, It’s the Mutation”].  Important biological changes occur in evolution only rarely, with most mutations not bringing about significant biological differences.  The progression of the spread of Ebola in 2014 was prolonged, involving as large number of human-to-human transmission events.  Under these circumstances, divergent evolution is guaranteed.  Each infection would lead to trillions of new Ebola viruses, and each transmission involved a genetic bottleneck, sampling a subset.  Both in the race to infect available cells in the host, and in chance opportunities for infection, Ebola viruses with meaningful genetic differences undergo competition.  Under these circumstances, the probability of adaptation to the host species (in this case, humans) was high.

The initial transmission of a virus from an animal host to humans is a change in the environment for the virus. Phylogenetic analyses conducted at the time showed co-circulation of several different types during the outbreak. Evolution needs three things to occur: (1) meaningful genetic variation that exists among individuals tied to survival and reproduction, and (2) time. The prolonged human circulation certainly led to an accumulation not only of differences, but to genetic variation, which drives adaptive evolution.

The GP-A82V mutation is non-synonymous mutation located at the NPC1-binding site Ebola glycoprotein (GP) mutant A82V. Analyses showed that the mutation existed early in the 2014 outbreak, and increased in frequency over time.  A study found that GP-A82V has heightened ability to infect primate cells. Cells that do not have the primate-specific NPC1 sequences at the EBOV interface are not as easily infected.  This supports that the A82V mutation is an adaptation to the human host.  Among infected individuals, GP-A82V was associated with increased mortality: the increased infectivity included human dendritic cells.  It’s almost as though the GP-A82V strain specifically disabled the human immune system.

Another study (Urbanowicz et al., 2016) confirmed these findings. Researchers generated a synthetic glycoproteins that represented the various lineages that circulated during the outbreak and put them into pseudoviruses.  These showed variation in their ability to infect various human and bat cell lines. GP-A82V had higher infectivity in human cells, and reduce infectivity for bat cells.

Figure1_ok

This is the phylogenetic tree (derived by the authors of the study) using data from A. Rambaut’s collection of Ebola genome sequences.  Important findings of both of these study include that adaptive mutation leading to this important amino acid substitution occurred early in the tree, and just prior to the exponential increase in the rates of transmission, and then went on to outpace the original genetic variant.  This means (to me anyway) that genomic surveillance early an outbreak should include infectivity assays using pseudoviruses so the most threatening types of Ebola (or other pathogens) can be most aggressively pursued.These two studies strongly support that the GP-A82V drove increased rates of transmission among people in West Africa.

A third study found two additional mutations, one of which, a D759G substitution in the active center of the L polymerase, increased viral transcription and replication (Dietzel et al, 2017).   They found another variant that led to decreased decreased viral transcription and replication.

Clearly, the specific mutations, not the rates, matter.

The lessons?

(1) During outbreaks, don’t focus on mutation rates.  Focus on transmission and mortality rates first. Those are phenotypes. With equal priority, focus on non-synonymous substitutions and perform functional assay analyses of those predicted (via computer modeling) to most likely effect protein structure.  Pour money into stopping the transmission of those suspected of being most transmissible, and have a field test available to determine, for each patient, the viral genome sequence.

(2) Don’t lie to scientists and to the public, and always put science before policy.  Every time.  Every pathogen.  Every vaccine.  Misinformation from the CDC prevented many scientists from looking further into available data on Ebola at time when EVERY scientist should have been looking, and such misinformation continues to prevent most scientists from knowing the reality of numerous out-of-date vaccines on the CDC schedule.

Such as this 2014 report that shows that most individuals who receive a whooping cough diagnosis are vaccinated.

Most scientists do not know it yet, but Tdap is a failed vaccine (see Epidemic Pertussis and Acellular Pertussis Vaccine Failure in the 21st Century) that has been expanded for use during pregnancy with insufficient safety data, and the CDC has not produce any data on fetal mortalities associated with the use of Tdap during pregnancy.  We need a new pertussis vaccine that excludes unsafe epitopes which are too similar to human proteins.  And we need randomized clinical trials that are sufficiently powered to detect adverse events with long-term follow up of total health outcomes awareness.  And they need to be conducted by research teams with no conflicts of interest. This Slate article shows how adverse events that might be attributable to HPV vaccine were excluded from consideration by Merck in data submitted to the FDA.  And two whistleblowers who claim that the MMR efficacy data was fudged by adding anti-mumps virus antibodies to fool the FDA into thinking the MMR was highly effective against mumps will shed more light in 2018 of the effects of putting profit and contracts before science.

And while we are considering misinformation from CDC, flawed policies matter, too.  Why is the flu vaccine only 10% effective, and how in the world can CDC recommend its use based on a hope for herd immunity?

Every scientist needs to know that thimerosal is in flu vaccines – some of them – and that thimerosal specifically inhibits ERAP1.  They need to know that CDC recommended flu shots w/thimerosal for pregnant women – preferentially.  Thimerosal not only contains ethyl mercury, which can induce neurodevelopmental disorders.  It also targets the human immune system protein that shortens proteins ERAP1-deficient cells have reduced surface levels of MHC class I molecules, and the peptide-MHC complexes that are made are less stable than on wild type cells – meaning thimerosal will make you more susceptible to infection from pathogens to which you are already immune.  This likely explains why people who get the flu shot are more likely to experience respiratory infection from non-influenza viruses.  And why getting the flu shot last year makes next year’s flu shot less effective.  So women who get the flu shot while pregnant may be more likely to experience high fevers due to infections. Maternal immune activation is dangerous.

My wishes for 2018: Scientists – bona fide, objective scientists, who in every other consideration of fraud conducted by Pharma on drugs will sign on, a swear that Pharma is corrupt, but who cannot allow themselves to transfer that perspective and when it comes to vaccines – to at least stop blaming the antivaxxers.  Vaccine fatigue is real. People with whooping cough and mumps are most likely vaccinated, and can become asymptomatic carriers. Vaccine safety science fraud is real.

And don’t blame mothers of vaccine-injured children for warning the world.  They are the most caring people on the planet.  They vaccinated.  Their child was injured.  The world refused to acknowledge it as an injury.  And yet they persist.  They continue to help raise vaccine risk awareness. And they won’t stop until vaccine risk is minimized.

We need to do much better in 2018. Because, if we are going to put science before policy, we have to do science.

I’ll be conducting research on ways to help kids learn to speak.  Because we want to know what all kids have to say. And on vaccine risk screening biomarkers to prevent vaccine injuries. Because vaccine injury is real, pervasive, and routinely neglected. And I’ll be facilitating and enabling research on safe ways of removing aluminum from our brains. Because amyloid in the brain is part aluminum (Nikaido et al., 1972; Masters et al., 1985; Yumoto et al., 2009).

MERCK1_2_HOLIDAY

References

Diehl, WE et al., 2016. Ebola virus glycoprotein with increased infectivity dominated the 2013–2016 epidemic Cell. 167(4): 1088–1098.e6.

Dietzel E, et al. 2017. Functional Characterization of Adaptive Mutations during the West African Ebola Virus Outbreak. J Virol. 2017 Jan 3;91(2). pii: e01913-16. doi: 10.1128/JVI.01913-16.

Masters CL et al., 1985. Neuronal origin of a cerebral amyloid: neurofibrillary tangles of Alzheimer’s disease contain the same protein as the amyloid of plaque cores and blood vessels. EMBO J. 4:2757-63.

Nikaido T et al., 1972. Studies in ageing of the brain. II. Microchemical analyses of the nervous system in Alzheimer patients. Arch Neurol. 27:549-54.

Urbanowicz, RA et al. 2016. Human Adaptation of Ebola Virus during the West African Outbreak Cell. 167(4): 1079–1087.e5.

Yumoto S et al., 2009. Demonstration of aluminum in amyloid fibers in the cores of senile plaques in the brains of patients with Alzheimer’s disease. J Inorg Biochem. 103(11):1579-84. doi: 10.1016/j.jinorgbio.2009.07.023.

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The Slaughtering of our Constitutional Rights

JOHN STUART MILL is sometimes attributed with the quote “Your right to swing your fist ends where my nose begins”.  In reality, the quote seems to have arisen during prohibition protests.

Everyone understands that there are times when individuals must be called upon to secure our liberties and rights as a nation, at the risk of cost to individuals. The military draft, for example, is seen by many as a necessary evil from time to time, but even the de facto suspension of individual liberties during the draft is seen as extraordinary – no draft would be acceptable during a non-emergency period. The draft, for example, would never have been acceptable during Bush’s elective war in Iraq.

Lately there have been moves on the part of governments and other organizations to reduce, limit, or remove individual liberties and rights, and a full accounting of which rights are impinged in the name of saving humanity from infectious diseases seems worth considering.

1st Amendment Right to Free Speech

I was stunned to read a legal “scholars”‘s treatment of the question of whether we should tolerate free and open discussion of questions of vaccine safety. Claiming that discussing vaccine safety was akin to “shouting gunfire in a crowded theater”, the authors of the article in the Jurist concluded that perhaps American citizens’ rights to discuss their knowledge of the risks of vaccination should be rescinded.

Luckily, the issue was aptly taken up by Mary Holland, a legal scholar at New York University, who wisely stated (in brief) that the right to yell “gunfire” becomes a moral imperative when gunfire has, indeed, erupted in a theater.

Rights to Informed Consent

Vaccine defenders trample all over individuals’ rights to informed consent for medical procedures, both inside and outside the doctor’s office. Inside the office, they routinely deny informed consent by minimizing what is known about risks of vaccine injury, both in terms of the diversity of injuries that may occur, and their frequency. Patients who ask too many questions about vaccine injury are seen as problematic, rather than being seen as exercising their right (in all states) to know specific risks.  Information on the known HPV vaccine adverse events provided by your doctor are incomplete, and if you ask for the vaccine insert, you will find that it, too states that it is incomplete in its listing of the known adverse events, and it refers you back to your doctor for a full list!

If patients or parents decide to exercise their legally guaranteed right (in 47/50 states) to refuse vaccination, or to modify the schedule, or to skip or delay any specific vaccination due to their individual concern over risk, they are treated as problematic by healthcare workers, including medical doctors and office staff. The disdain and disregard for the law in such a setting by medical professionals is obvious.

California bill SB277 is a highly contested example of a state overreaching the authority intended by previous cases. It specifically strips Californians of the right to non-medical exemptions, and those who persist in exercising their Federal rights to refuse medical treatment once fully informed of the risks are stripped of their rights to access a public education, a right specifically provided by the California state constitution.

AAP Codifies Patient Harassment and Abrogation of the Hippocratic Oath

Doctors and healthcare workers around the country have been reported to use coercion, shame, and threats to deny patients access to medical care if they are vaccine-risk aware, and choose any of the legally provided options other than the CDC schedule. Last week, the AAP codified this disregard for the law by approving pediatricians’ practice of refusing to provide medical treatment to citizens who exercise their legal rights to non-medical exemptions. Citizens in nearly every states with mandatory vaccination for school attendance have the right to exercise religious, philosophical, moral and personal belief exemptions, whether pediatricians like it or not.

eximmunmap15-tuesday

Sept 2016: Forty-seven states honor individual and parental rights to refuse vaccination – without their doctor’s permission to do so. AAP, CDC, and Pharma want that number to be ZERO.

In some states, the medical community has tried claim that doctors should ascertain for the state whether a person’s request for a religious exemption is genuine. Such laws and practices  are clearly a violation of the freedom of religion, which is a constitutionally protected right provided in the religion clauses of the First Amendment.  A moment’s review of the contents of some vaccines (aborted fetal cells, pig products) will reveal that recipients who are forced to receive those contents into their bodies are also being forced to deny central tenets of their faith.

Across the US, patients are denied informed consent in myriad other ways as well.  The fact that pharmaceutical companies are exempt from liability prevents news stories of companies held accountable for harm – and also prevents motivating companies from making vaccines safer.  Instead, consumers pay a tax on every vaccine to pay damages via the National Vaccine Injury Compensation Program – which sounds good, until one realizes how extremely tortured the logic has been to make vaccine-induced encephalopathy a replacement vaccine injury for autism so the program does not have to pay for vaccine-induced encephalopathy-mediated autism.

Right to Refuse Medical Experimentation

After the Nuremberg trial, it became both common international and national law in the US that no citizen shall be subject to medical experimentation without their express, fully informed consent. The law that protects American citizens’ right fall under the FDA’s domain, which requires that all medical researchers conducting human subjects research acquire specific consent after reviewing the full list of known and potential risks associated with experimental drugs and medical procedures.

Much of what the CDC calls vaccine safety research is conducted using post-market surveillance. US citizens are not informed that their reaction to a given vaccine may be used by the government or government-funded researchers to assess vaccine safety. By definition, then, we are all enrolled in an uncontrolled medical experiment without consent. We are never given the opportunity to refuse to be enrolled in this massive medical experiment. Not that it matters much for the sake of the science; the studies conducted using data from the passive Vaccine Adverse Events Reporting System (VAERS) and the Vaccine Safety Datalink (VSD) are nearly universally retrospective descriptive correlational studies, and thus any suggestion or hint of increased rates of serious adverse events can easily either be cooked away by repeated rounds of data analysis (analysis-to-result), as has been the practice at the CDC for studies on the question of vaccine-induced encephalopathy-mediated autism, or the results can be dismissed as merely ‘correlational’.

When a new vaccine is being added to the CDC pediatric schedule, the prospective studies that are conducted do not test the cumulative effect of the vaccine schedule against unvaccinated individuals, but rather existing schedule vs. modified. Those that do use ‘placebo’ tend to use the adjuvant (additive designed to enrage the immune system) vs the vaccine, and thus the rates of mild, moderate and serious adverse events for vaccines are unknown.

13th and 14th Amendment Rights: The only way so far to identify individuals – and families – who are at risk of vaccine injury is to vaccinate them, and thereby injure them. These subgroups of individuals are potentially identifiable – if only research priorities allowed us to focus on the development of biomarkers to predict who might be at risk of specific harm. In America, minority citizens have, under the 13th and 14th Amendments, the rights to equal protection. The first step to predicting who among us are at special risk is to admit that vaccines cause harm. In denying the link between vaccines and autism, not only are the rights to informed consent denied, and rights to compensation for harm being denied, but the right to protection by the state as a genetic minority are also denied because the science to identify specific biomarkers for specific serious adverse events for specific subgroups cannot be conducted when autism denialists write the rules.

CDC Proposes Their Totalitarian Rule

In a stunning move made under the guise of medical emergencies caused by emerging infectious diseases, CDC has proposed new rules for themselves to be able to apprehend and detain American citizens indefinitely, without access to legal counsel; to disallow citizens’ rights to cease communicating with the CDC (First Amendment; Fifth Amendment); to access (without consent) our electronic communications (Fourth Amendment); to forcibly vaccinate American citizens against their will (Rights to Informed Consent); and to deny them any compensation whatsoever for any harm done to them physically  or to their attempts to enjoy their rights to life, liberty and the pursuit of happiness.  Defenders will say that this is only for instances in which an emergency has been declared, and they list specific diseases for which they imagine they may have to impose totalitarian rule (Ebola, Marburg, and others (see a full accounting by James Grundvig here). They also, of course, give themselves the right to add more diseases, and thus vaccines, to this list. CDC wish to grant itself open-ended police powers in a manner that is not only not consistent with the Constitution: their power grab is not consistent with America.

I am sure that I have not fully counted the number of rights seized by the CDC Totalitarian Rule, but they must be stopped. They should not be granted powers to suspend most of the Constitution.

CDC employees have an odd, paramilitary culture that is not necessary in a free and open society.  Perhaps they are nervous and this bluster is a threat. Perhaps they will apprehend people who write blog articles. Perhaps they will apprehend people who make movies. Perhaps you will be arrested by a Rear Admiral and force-vaccinated against all of these diseases because you told your sister about “The Environmental and Genetic Causes of Autism“.

We must immediately, forcefully and collectively assert and affirm our rights to:

  • Rights to Free Speech
  • Religious Rights
  • Rights to Refuse Medical Treatment
  • Right to Refuse to Participate in Medical Experiments
  • Rights to Equal Protection
  • Life, Liberty and the Pursuit of Happiness.

Summary

The reality is that open-end legislation at Federal, State, and County levels on vaccine mandates are dangerous, because no science is done to tell us about the risks of adding an ever-increasing number of vaccines, and this newly proposed ’emergency’ authority to force vaccination upon American citizens a list of vaccines to which CDC can add at their whim cut deep across the grain of American sensibility and our traditional respect for the rights of individuals.

The attack on Constitutionally guaranteed and protected rights being visited upon the American public is sometimes described using the word “impingement”.  The aggregate effects of these moves is not an impingement – it is a dismantling of our safeguards against a totalitarian state. It’s a wholescale slaughter of the Constitution.

What are your thoughts? What other rights are being threatened by vaccine risk denialists?  Let’s have #thediscussion – while we still can.

References

The Constitution of the United States of America

Holland, MS. 2011. Legally Censoring Speech on Vaccines and Autism: A Response. The Jurist http://www.jurist.org/forum/2015/12/mary-holland-vaccines-autism.php

Vaccine Safety Datalink


About the Author:

Dr. Lyons-Weiler is the CEO of The Institute for Pure and Applied Knowledge, former Senior Research Scientist and Scientific Director of the Bioinformatics Analysis Core at the University of Pittsburgh, and former faculty member in the Department of Pathology and Department of Biomedical Informatics (University of Pittsburgh), and former full faculty member in The University of Pittsburgh Cancer Institute. He is the author of three books (Ebola: An Evolving Story; Cures vs. Profits: Successes in Translational Research and The Environmental and Genetic Causes of Autism). To book Dr. Lyons-Weiler for speaking engagements, email ebolapromo@gmail.com

Visit Dr. Lyons-Weiler’s Facebook author page.

My Journey from Ignorance

WHILE RETURNING from the United Nations building where I heard NYU Professor Mary Holland (School of Law) nail the issues of constitutional and international law on the right to informed consent to the floor, to a standing ovation, I received an email from Mary ( To my delight). I read, in part:

“I  started reading your Ebola book last night.  Wow, you have evolved a lot in your thinking on vaccines in a VERY short period, based on your definition of ‘antivaxxers’ at bottom of 206, top of 207.  Have you written up how your views evolved so quickly?  It might be a helpful roadmap towards turning others around.  Was this all in connection with the autism book, or did your views changing precede that book?”

Looking at my book this morning, I turned to page 206, with trepidation, to find the younger, knowing me, trying to save the world by chiding and deriding people whom I have come to learn much more about in the past two years:

“Again and again with Ebola we see, from Guinea to the US, societies struggling with the ethical problem of the needs (and wants) of a few vs. the safety (and lives) on the many”.

Ok, that’s not too bad.  A bit uppity, but I cannot disagree. But it gets worse.

“With over 100 cases confirmed, the US is, at the time of this writing, at high risk of an epidemic of measles because the herd immunity is lacking due to a dogmatic antivaccination movement”.

I warned you.

Deplorably, I continue:

“The efficacy of the measles vaccine in protecting children against terrible diseases should be reason enough for parents to insist on vaccinating their children, but the so-called ‘anti-vaxxers’ (people who believe vaccines place their children at risk of developing autism) fail to consider the greater good: They put others at risk by not participating in national programs for the greater good.”

I really do not like my former self. Naturally, I continue, because I knew SO much before I actually looked into the studies and the data:

“This perspective is more than mere 20:20 hindsight; such occurrences of cultural and institutional amnesia are certain to recur as our society becomes more reliant and trusting in technology, and we forget to respect the awesome power of biology and Nature”.

I really don’t know this guy, I swear.

Mary Holland will certainly be remembered as one of the most staunch defenders of human rights, well, in the history of abuses in medicine. So back to Mary’s question:

“Have you written up how your views evolved so quickly?  It might be a helpful roadmap towards turning others around.  Was this all in connection with the autism book, or did your views changing precede that book?”

Here’s how and why my views have changed. First, I was really rather upset about the fact that CDC Director Thomas Freiden stated in his testimony to Congress that there were no mutations in the Ebolavirus that was driving the epidemic.  I was upset because I had the 396 mutations on my laptop at the very moment he testified to Congress.  I capture that moment in “Ebola“. My anger at the CDC increased when I attended a secret White House conference call, held by the Ebola Czar, in which I asked about the 396 mutations – whether they influenced the ability of tests to detect Ebola, or altered its virulence or transmissibility. In that call, the entire scientific community was lied to again by a CDC Scientist who claimed that the virus was “99.9999% identical to the strain from Zaire in 1995”, which was not true at all.  I capture both of those events in “Ebola”, as well as how the White House then asked the Associated Press to stop covering potential cases of Ebola in the US.  I even ask in that book whether that was “fascism”.

Fast forward a couple of months to where I had decided to write “Cures vs. Profits“. I felt that we had bungled our response to Ebola so badly that I wanted to cheer myself up and write a book on the successes in biomedical research.  Having participated in so many studies over the past two decades, I knew of many reasons that the public should continue to support biomedical research, and I was going to share all that I knew, and discover more. The first two chapters deal with “the bad stuff” – the doctors who cheat at medicare fraud, which robs other patients of needed funds for real medicine – and the biomedical researchers who cheat at their research studies.

I wrote my chapters out on grapefruit, on cancer vaccines, on prostate cancer robotic surgery, and then something happened: I wrote a chapter on ADHD overdiagnosis. I tell the story of the destruction of a promising career of Dr. Gretchen Watson.  Pharma sent a “Key Opinion Leader” to EVMS to debate her over her study, and the next day she was told her case load was canceled, that her colleagues were told that she no longer worked at EVMS, and that she was to expected to resign.  She refused, and won an appeal to HR.  But then someone floated a rumor that she manipulated her data in the 1996 study showing overdiagnosis.

The investigation revealed no flaw – well, a typo in an appendix – but the damage to her career was done. The good news is that Dr. Watson has decided to write of book of her own after reading my chapter on ADHD.  She now also serves on the Board at IPAK.

When I finished writing the rest of “Cures“, including chapters on the history of hormone receptor status in breast cancer, chemosensitivity assays, characteristics of good research scientists, and cancer vaccines, I found the book missing something.

So I decided to write a chapter on Vaccines.

I’ll let the chapter on vaccines speak for itself- it begins with tales of how wonderful vaccines are, how they save lives.  I went back to review the autism/vaccine link, fully expecting to review the Andrew Wakefield issue briefly, how his claims that MMR were linked to vaccines. I read the retracted study.

I found that Andrew Wakefield never claimed that the MMR might cause autism.  Instead, I found the study to suggest that it was a question worth looking into.

My digging around then led to my discovery of reports that someone at CDC had revealed that CDC had manipulated data on the studies designed to disprove Wakefield by omitting results with a positive association.

The more I dug into the issue, and then into the literature, the more I found the science of vaccines falling far short of the science needed to insure public health via any medical procedure given to millions. And this is where I leave the issue in “Cures“. I added an addendum that reviews four open controversies in vaccines that cause me to question whether vaccines can be called an unmitigated success in translational research.

In retrospect, I see that position as something of an understatement.

My understanding of vaccines was (obviously) limited, and I needed to grasp the risks involved. I needed resolution. So after I completed “Cures“, I began writing about what I had learned. I spoke with people with an open mind. I started to listen not only to what these evil, selfish “anti-vaxxers” had to say, I started to really think about the consequences of the additives. I began to question the over-arching claims of safety.

And via some new contacts, I made connection with Tony Lyons of Skyhorse Publishing. After a few chats, he, Louis Conte and I agreed that I should write a book on the Genetics of Autism. (I love Louis – and knowing what I know of him now, my bet is that he thought I was a good prospect – but somehow I can hear him telling Tony that Jack has ‘a way to go, but I think he’ll get there’. Thank you Louis for the confidence.

So in I dove, into 3,000 research articles on autism.  Not on vaccines – on autism.  I wanted to know if the basic science could in any way reasonably support a hypothesis that vaccines or their additives cause autism. The answer is a resounding “Yes, yes, and yes”. Other articles in this blog will give you an idea of some of the evidence that exists on the role of chronic microglial activation and autism, for example.

To the readers of “Ebola” who feel confused or hurt by my, and others’ ignorance, please remember that there is a Great Unknowing, even among professionals.  Think about it – all “Anti-vaxxers” with vaccine-injured children were once pro-vaccine. As I advised some 500 participants at the VIALs Health Summit in Atlanta, GA, do not argue with them – educate them. Your anger and frustration is warranted, but help them move from ignorance to awareness and understanding.

I took it upon myself to consider 3,000 articles on autism for “Causes” (available at Amazon.com and in your local Barnes and Noble or indie bookstore).  (I skimmed 3,000, read >2,000, and cite >1,000). Look at what knowledge can do to a scientist who themselves feel cheated and lied to, someone who entrusted the CDC to perform objective science (See “The Tyranny of Pseudoscience“):

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The author at a CDC Rally, April 22nd, 2016.

 

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Educating the public and calling for Congress to Subpoena Dr. William Thompson at the CDC on the true nature of so-called “Science” conducted at the CDC on the link between vaccines and autism.

To My Fellow Scientists and Medical Health Care Professionals

I wrote “Ebola” in good faith, assuming that the position of the CDC on vaccines was based on sound science. It was unfathomable to me that

-Upon finding positive associations, CDC would routinely over-analyze data from studies until they could make associations go away, and when they could not succeed in doing that, they would simply omit the results;

-CDC would suspend an employee who drew these practices to the attention of then CDC Director Dr. Julie Gerberding (who subsequently took a position in charge of vaccine development at Merck);

-After CDC published these studies they called for an end to research on vaccine safety with regard to potential links to autism;

-CDC would ignore nearly all of the basic science that shows mechanisms of how neurotoxins in vaccines (not just MMR) could reasonably be expected to cause autism in some people;

-CDC’s position is based on ecological association studies, not randomized prospective clinical studies with proper controls.

-Our knowledge of vaccine safety is based on post-market surveillance;

-CDC would ignore all of the post-market surveillance on vaccine safety, claiming that the passively collected data in VAERS did not provide causal evidence;

-CDC would lie repeatedly under oath to Congress about the State of Science on the link between vaccines and autism;

-No one has ever conducted a vaccinated vs. unvaccinated study for association with negative health outcomes, including autism.

-CDC would communicate to the public that “Vaccines Do Not Cause Autism” on their website knowing full well that 6/12 vaccines on the schedule before the age of 7 have 0 studies one way, or the other, on whether they indeed may (or may not) contribute to the risk of autism.

I, like the rest of the world, relied on the CDC to be a reliable source of information on vaccine safety.  Yes, I vaccinated my children. I will not allow them to get the HPV vaccine. Here is why.

To the Parents of Vaccine-Injured Children who Regressed Into Autism

Your observations are the basis of a new era in vaccine science.  All science begins with observations. Help and relief is on the way. And there is nothing that can stop it.

IMG_0573
Dr. Lyons-Weiler (right) meets Marcella Piper-Terry (left) at the 2016 CDC Rally.
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Fellow Vaccine Risk Aware Protestors Calling for Congress to Subpoena Dr. Thomspson
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Dr. Lyons-Weiler meets the future Director of the CDC.

After the Rally, we enjoyed a summit at Life University hosted by VIALS. Here was our audience:

20160423_174651

Here I presented the CDC Schedule as backed by “Magic”, because no science exists on any link between 6 vaccines and autism, whereas some vaccines do, in fact have some studies that support association:

no science 2no science

That was a good day in Atlanta, GA. Here are the slides to share with your pediatrician:

VIALs health summit slides James LyonsWeiler MAGIC

CDCSCHEDULE
“MAGIC!!!”

 

 

Next stop, the United Nations:

 

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Dr. Lyons-Weiler attends a UN Session on Toxins in Our Children, April 26th, where Dr. Thompson’s revelations were shared with the world.


 

Mary Holland standing up for your rights to refuse medical procedures as a basic human right. To watch the unprecedented UN Session on Toxic Contamination of Children (4/26/2016), follow this link.

Mary Holland’s question to me was an important one:like many, if not most other professionals, I had argued my position on the vaccine/autism question from a position of ignorance.  They simply have not done their homework, and many have bought the CDC’s lies hook, line and sinker. They count on CDC to be honest and forthright. This include the AAP, the AMA, and, very likely, your pediatrician.

Most of them probably have not read a single study. They likely have never read the following words that Dr. William Thompson said to Dr. Hooker:

Thompson: “They don’t really want people to know that this data exists.”

Thompson: “…among the blacks, the ones that were getting vaccinated earlier, were more likely to have autism.”

Thompson: “It appears in the final publication is that race in general is downplayed. Of course it is.”

Thompson: “I actually think the most interesting results are the isolated, ones that don’t have their co morbid conditions. The effect is where you would think it would happen.”

Thompson: “I was just looking at—I was like, oh my God, I cannot believe we did what we did. But we did.”

Thompson: “The higher ups wanted to do certain things and I went along with it. In terms of chain of command, I was number four out of five. “

Thompson: “…Literally, everyone else got rid of all their documents, and so the only documents that exist right now from that study are mine.”

Thompson: “There are things that I haven’t even shared with you because I can’t prove it, and that’s what I struggle with. I don’t want to share things with you that I can’t prove, that there aren’t hard records. I am worried that the other four people will collude and say no, that’s not true.”

Thompson: “That’s what I keep seeing again, and again, and again where these senior people just do completely unethical, vile things and no one holds them accountable. “

Thompson: “The reason you don’t see anything else circulating on the study, it was five of us behind closed doors for two years.”

Thompson: “It’s the lowest point in my career that I went along with that paper.”

thompson_CDC
Dr. William W. Thompson

My book “Cures vs. Profits” tells more of the story of Dr. Thompson and Hooker. At this point, I am willing to go on the record and say that I have zero – ZERO confidence in any science coming out of the CDC Immunization Safety division. And no one else should trust their research, either.

In fact, nothing they publish can be trusted. Not merely because of what Thompson said.

I’ve read their studies.

They are atrociously unsafe ventures in data cooking, model overfit, sad excuses for “control variables”, use of multicollinear variables, the product of repeated data analysis to a desired result (no association). They are a mess.

The individual people in question include

RADM Anne Schuchat, Principal Deputy Director of CDC

Dr. Frank DeStefano, Director of the Immunization Safety Office

Dr. Coleen Boyle Director, National Center on Birth Defects and Developmental Disabilities (NCBDDD)

Dr. Poul Thorsen (co-author on suspect CDC studies, wanted by HHS for embezzling over $1Million in funds that were to be used for autism research, living openly in Denmark).

and others.

In my research, I strive to remain objective. However, since 2004, when the research fraud at the CDC occurred, there have been over 1,000,000 cases of autism that potentially could have been prevented simply by splitting up the MMR into three vaccines, spacing the vaccines out, giving non-adjuvanted vaccines with 1 adjuvanted, screening for safe epitopes, removal of mercury from all vaccines, giving medical exemptions to parents who already have one autistic child (to avoid the genetic x environment interaction), dropping HepB until adulthood… so many simple things that could have been done to reduce early exposures to toxins. Where is the science for biomarkers to indicate which children might be most at risk of ASD due to vaccines?  Not done.  CDC called for no more science.

We Want Evidence-Based Public Health Policies, not Policies Based on Subjective Belief (aka “Magic”)

Right now, the so-called “Anti-vaxxers” I so woefully admonished in “Ebola” are not all “Anti-Vaxxers”. They do consist partly of some people who believe no safe vaccine could ever exist. I respectfully remind them that until the science is done to show that non-adjuvanted vaccines without mercury, aluminum, formaldehyde, etc are tested, their knowledge claim is an untested generalization about all vaccines. Out of well-deserved distrust, they call for no more science on vaccine safety – because they know that some will be injured by that very research.

But the Vaccine Risk Aware movement also includes people who are 100% Pro-Vaccine Safety. They suspect that safe and effective antigen presentation systems can be designed, that use exposure at the skin (microdermal abrasion), with epitopes that do not induce autoimmunity. They believe that taking the toxins out will likely make vaccines safer. But they do not make such claims.  They call for more science, not less, but on newer options for inducing immunity.

To watch my presentation at the VIALS Health Summit State of Science on Vaccine Safety: Autism, in which I explain how the CDC’s claims that vaccines do not cause autism must be based on magic, follow these links: (Part 1, Part 2, Part 3).

Calls for Retraction of CDC “Studies”

Because CDC committed scientific fraud, the studies they performed should be retracted. IPAK has informed the journals of this, and we have sent them copies of “Vaccine Whistleblower, by Kevin Barry, Esq.

I urge all of my colleagues to view the movie #Vaxxed.  Call your local theater and ask them to screen the movie. If you consider yourself an objective scientist, read “Whistleblower“, and RFK jr.’s book, “Thimerosal: Let the Science Speak“.  Order “Master Manipulator” by James Grundvig, which tells the story of Poul Thorsen, a CDC collaborator wanted for absconding with autism research cash (given what CDC would have done with the money, Thorsen may be a hero, for all we know).  For a deeper timeline view on how long corporate corruption has eroded science in our most esteemed institutions like the CDC, read “Science for Sale” by David Lewis.

I ask my professional colleagues from all walks of science and medicine then to join us in our calls for retraction of the CDC’s false studies: DeStefano et al., Madsen et al., and Verstraeten et al.  I will not stop educating professionals about the fraud because we need evidence-based medicine, not medicine based on guesses, or hopes, or magic.  Babies are dying in the womb due to mercury in flu vaccine reserved for pregnant women; babies are born autistic due to immunoneuroexcitotoxicity; they are born with seizure disorders; toddlers regress into autism after learning language. And yes, it may be due to cumulative and interactive effects of toxic chemicals from agriculture, industry, our home, etc.  But we can reduce the toxins we expose our children to.  Right now, autism risk is 1 in 68, up from 1 in 3000 in the 1970’s.  Let’s have #theconversation.

MeetingCropped

 

Acknowledgements. I have literally thousands of people to thank for helping move from ignorance to awareness.  You know who you are. Thank you.

Please support VIALs with a generous donation.  Tell them Jack sent you!
To support Dr. Lyons-Weiler and his research associates at IPAK, visit ipaknowledge.org

VIALs health summit slides James LyonsWeiler MAGIC

causes

Ebola Evolving: It’s Not the Rate of Evolution, It’s the Substitutions

A NUMBER OF STUDIES have reported results from the analysis of the genomic sequences of Ebola, acquired from patients in the 2014-2015 outbreak/epidemic.  The authors suggest that because evolutionary rates have not increased relative to those observed in past outbreak of Ebola, the virus has not and is not becoming more pathogenic.  They conclude that there is not, as originally reported [4] an increase in the overall mutation rate. Therefore, the presumption is, it is not acquiring new characteristics that would make it something more likely to cause death and wreak havoc on societies.

These reports also reassure us that because there are few non-synonymous substitutions relative to synonymous substitutions, natural selection is not likely to be necessary to invoke as a factor.  I.e., again, the virus is not ‘adapting’, and, therefore, because it is not becoming more fit to infect and spread among us, we can relax.

The press dutifully reports, and extends the conclusion, to reassure use that, for example, Ebola is therefore not likely to “go airborne” [5,6,7,8]. [See Ebola: An Evolving Story to find out why that is not the most interesting question to ask about Ebola evolution in the first place.]

As a life-long student of evolution, endowed with a PhD in Evolution (among other things), I understand where they are coming from. That is, I understand what they are talking about. Before jumping into biomedical genomics and genetics, I enjoyed two years in a Post-Doctoral position with Dr. Masatoshi Nei at Penn State University.

However, based on my understanding of evolutionary processes, I have no idea why they come to such conclusions looking at mutations, mutation rates, rates of nonsynonymous/synonymous substitutions. Here are my observations on the matter:

(1) It will very well understood that the limit on the rate of evolution – i.e., the rate at which gene frequencies can change over a specified (long) period of time – comes from the mutation rate.  Dr. Motoo Kimura demonstrated this elegantly with mathematics with which every card-carrying evolutionary biologist should be familiar. Therefore, unless some factor has led to an increase in the error rate of polymerase, DNA repair enzymes, we should not expect an increase in the observed overall mutation rate (influx).  This virus hijacks, of course, our polymerases and post-replication mismatch repair enzymes. Thus, unless our polymerases and DNA repair enzymes have mutated in some way, we cannot expected increases in mutation rates.

(2) Selection removes variation, and adaptation does not always “increase” a phenotype.  To the extent that mutation rates and evolutionary rates themselves are adaptive, a slow-down in the overall mutation or evolutionary rate could easily be adaptive in the right environmental context.

(3) Looking at NonSynonymous and Synonymous substitution rates is, generally, good way to measure positive Darwinian selection over long periods of time, to identify which genes may have been influenced by positive selection (that which drives rare alleles to fixation) .  However, some mutations (such as the variant found in position 10,218 in the original Gire et al study) may not encode an amino acid at all, and could influence phenotypes other than those expressed via proteins. Viral phenotypes include replication rates, and Ebolavirus genome functioning including RNA expression includes some unusual features, such as ‘stuttering’. The GP gene encodes two “genes”, the large, GP gene, and a small sGP gene that is expressed at high ratio to the GP gene.  The sGP protein is small and can confuse with misleading antigenic signal, or overwhelm the immune system with sheer numbers.

(3) Random gene frequency fluctuations occur in populations of small size. Ebola has anything but small population sizes. In my book “Ebola: An Evolving Story”, it is explained that new virus particles infecting a human (or gorilla, chimp, or bat) is akin to a lifeform colonizing a new planet.  In the few short (3-4) first days of infection, viremia can rise from nothing to billions of copies per mL of blood. Thus, random fluctuations, and random fixations, are not likely to occur.  It is very difficult to move gene frequencies around by chance in large populations, and the selection coefficient must be immense for alleles to march from next to nothing to fixation.  “What about the repeated genetic bottlenecks?” you might wonder, speculating that transmission usually involves perhaps a few viral particles. Putting aside the reality (it varies – a lot), let’s assume each transmission involves a handful of virus particles in the hot feces or vomit that someone inadvertently is exposed to.  In the growth phase of the epidemic, the sampling process, if done by chance, occurs repeatedly and independently in different branches of the expanding population.  However, the sampling frequency of alleles, if by chance (and that’s important, first assume equiprobable transmission of all viral particle, regardless of genotype) will still be based on their standing frequency within a person at the time of transmission. Each person has hundreds to thousands of quasi-species, most at low frequencies, due to the introduction of new variants via mutations. The new quasispecies that contain new variants will be, independent of selection, at low frequency (initially 1/N). Variants that happen to occur at the beginning of an infection have a much higher likelihood of drifting to fixation by chance (drift); but none of them have the starting advantage of the founding quasispecies (which at the time of the new mutation will be m/N). Any given quasispecies at any given time will have a frequency of n/N. typically, m/N will be nearly 1.0.  Therefore, the probability that the primary quasispecies will transfer will be nearly 1.0

In a growing population, drift is rare; resources (us) are abundant, and positive Darwinian selection can be expected to be rare. It’s when resources become scarce – all of the available tissues are infected, all of the people are immune or sick and dying, or dead) when competition between genotypes becomes most intense.  However, if there are any mutations at the onset of a zoonotic transfer that gives even a rare quasispecies a strong advantages in terms of faster rates of transmission (higher RO), faster rates of replication within a host, more optimal (fast or slower, depending on the fitness function) replication rates, which tissues it infects earliest in the progress of the diseases… there are myriad ways other than going ‘airborne’ for a virus to become more nasty (more virulent, more infectious, or even less virulent if it means it will infect more individuals).

Many high-ranking officials will report that there is “no evidence” of any change in transmission mechanism. This position ignores the often reported shift in the symptomological spectrum of Ebola this time around compared to 1995. Reliable data on symptoms may be hard to come by, but most reports this time around noted much, much more severe, sudden onset (without warning) vomiting and diarrhea compared to 1995. Let’s for a moment say that the plethora of reports of shock at the rate of spread, the large percentage of health care worker deaths, and the sudden symptoms are not reliable.  Which side of a debate where one claims “neutral evolution” and the other claims “adaptive, Darwinian selection” is going to be able to demonstrate, convincingly, from genomic sequence analysis alone, that their position is the correct one?

Evolutionary biologists studying sequences need to be careful, and the press needs to be especially careful, when considering the interpretation of the analysis of sequence data. In particular, they need to pay attention to precisely which sequences from the epidemic are being analyzed, where they were collected from, and, importantly, when in the outbreak or epidemic they were collected.

The first data [1] out came from the first passages (transmissions) in the outbreak. This period of evolution is distinct from other periods of time;  pre-transfer to human, the primary quasispecies resident in the host would have been sampled at a rate of m/N, and any minor quasispecies would have been sampled at a n/N.  As the virus passed from person to person, the sampling rate of m/N would continue to predominate, unless or until a rare quasispecies became the primary in a person (either via drift or selection).

Within each person, the burgeoning population of quasispecies would typically continue to reflect a mix of the sampling of 1, 2 or maybe 3 quasispecies, and any new quasispecies that evolved via mutation while the trillion-sized population grew. With each new infection, the sampling game would continue, person after person, at a rate of {m/N, n1/N, n2/N, n3/N…no/N}, with the outcome of each sampling effort leading to a new constellation of m’s and n’s in their relative ranking.

A key question is that whether repeated bottleneck driven genetic drift, or via Darwinian selection, is behind the observed change in the frequencies of quasispecies and alleles over time. Given the billions of copies of Ebola in infected persons’ bodies at the time of transmission, genetic bottleneck is very, very unlikely to drive a rare mutation (such as the variant at non-coding position  10,218) to fixation in a serial passage situation.

In that first study, the novel allele at position 10,218 was observed, in this supposedly random, haphazard sampling game of allele frequencies, to march, seemingly deterministically, against all odds, toward fixations as the disease coursed through 96 people. This allele, a non-synonymous substitution is of unknown functional significance.  The allele was original found in 12 people, and was observed to increase in frequency to become fixed (the only variant) in 38, one of two variants in 12 patients, and absent in 28). The allele was found in another analysis to separate a fast-spreading Clade 3  from a slow-spreading Clade 2 (See the L. Bedford’s Lab “Is Ebola Adapting?”).  The variant increased over time, and was observed to cluster geographically and in the transmission chain.

A very recent paper (Park et al., 2015) analyzing more sequences mentions variant 10,218 and the third clade, which they describe a more complete picture of 10,218 as SL3, as follows (emphasis mine):

“A third lineage (SL3), derived from SL2, emerged in mid-June 2014. SL3 differs from SL2 by a single mutation at position 10,218, first found as an intrahost variant (polymorphism within one individual) at a low frequency. SL3 became the most prevalent lineage in Sierra Leone during the first 3 weeks of the outbreak there, with SL1 disappearing soon after the appearance of SL3. The SL3-defining mutation is epidemiologically important, as it is the first commonly circulating mutation observed to arise within Sierra Leone’s borders.

As the epidemic developed within Sierra Leone, the SL3 lineage continued to dominate the viral population within the country, with no evidence for additional imported EBOV lineages. In our data set, 97% of the genomes carry the SL3 mutation and the remainder belong to SL2.

Any allele that has gone from new to 97% of all genomes in the face of repeated bottlenecks during transmission is very likely adaptive. This constantly increasing frequency of all allele over time, and its association with a greater rate of spread, during the supposedly random sampling series is consistent, probabilistically speaking, with natural selection, and is by far much less consistent with neutral evolution via drift. The key here is to recall that we are talking about repeated bottlenecks from very large population sizes, and that it is very, very difficult to move gene frequencies in large population sizes.  Repeated bottlenecks can be effective at fixing common alleles, but the effectiveness of drift at fixing each allele in the founder population is equal that allele’s frequency in the parent population.  So, on average, in the Ebola scenario. we should not see nearly perfectly linear increases in a rare allele frequency toward fixation unless there is something driving it. Studies of the functional significance of 10,218 should be undertaken.

Just like the focus on ‘airborne’ as a mode of transmission detracts from consideration of other evolutionary avenues, the focus on the overall evolutionary rate confuses that fact that selection will tend to increase the rate of turnover of rare frequency alleles into high frequency, potentially fixed alleles, but not (necessarily) rate at which the total number of substitutions observed might occur. When a zoonotic transfer takes place (aka, “spillover’ a la David Quamm}, the alleles may in fact quickly sort themselves out based on the contribution of each allele to each viral particles’ within host fitness (so-called antigenic pressure, competition among quasispecies, etc.). The relative time frame can be counted in terms of passages. It can take a surprisingly low number of passages to see a virus adapt to the new host. However, once this initial adjustment to a new environment is made, the virus might then be expected to settle in, and thus would could expect that overall turnover rate or genetic flux rate might slow back down. In transferring to humans, the virus has landed on what Sewall Wright

Adaptive Landscape 1 tif to jogcalled an “Adaptive Landscape”, with various fitness peaks to travel up, reflected by the environment. If the mutation of interest (10,218) causes Ebola to cause enteric disease at an earlier stage of the disease than other hemorrhaging, and other mutations cause a prolonged incubation period before any symptoms, Ebola could spread faster either by making people either less sick, or sick in a slightly different manner.

Evolution of Virulence and Infectivity, or, more Precisely, Evolution of Pathogenicity and Morbidity

One such view on the adaptive landscape become apparent when one simultaneously considers the evolution of pathogenicity (the ability of the virus to make a person sick) and morbidity (the ability of the virus to cause diseases and deaths in a population).  Thinking of the rate of transmission, risk of infection, and the ability of the virus to travel from person to person, we can see that any virus with high pathogenicity in an person would quickly die out, killing a few members of a host species, and taking itself with them. Thus, the expected adaptation in Ebola would be toward less pathogenicity, not more. The influence of a less pathogenic virus could mean that it could survive longer, infecting more people, and still be relatively pathogenic, and could kill many, many more people.  So the news that there was a first a rapid rate of evolution, followed by a slow down, are hallmarks of rapid adaption to the virus “learning” how to persist in our species via selection.

In fact, it was the later studies that showed this. The press takes the later studies to mean that the initial study was wrong.The latter studies that show a slow-down do not impeach the previous results showing rapid adaptive evolution.  They augment them.

And the news that monkeys infected with ebolavirus from 2015 become sick 2-3 days later than those infected with the 1976 virus is not necessarily good news either, especially if there is even a small amount of pre-symptomatic transmission, or people live longer with a slower-progressing disease, shedding virus for many more days than in 1976. (See Are Data from Ebola Studies Still Being Misinterpreted?)

It’s the Substitution, not the Rate

Moreover, a mere handful of mutations could cause these phenotypic changes. With an virus as complex as Ebola (for all of its seven known genes, each with more than one known function), adaptive evolution could involve as low as a single substitution. It has occurred it me that the one allele that allows one of the virus’ proteins to fold in a manner that causes it to functional as an analgesic, or a painkiller, causing a drop in the stomach pain prior to vomiting or having diarrhea. Perhaps a second mutation would make the viral more enteric and less hemorrhagic.

That is not much molecular change.

So, a more appropriate tagline in the press would be “Scientists find evidence of possible evolution of higher morbidity in Ebola via increased transmission dues to lowered  pathogenicity” would help understand the possible risks of attendant to our species due to evolution in Ebola since the onset of the epidemic. It’s probably a good thing I’m not in charge of press headlines.

The problem is that the analysis of molecular data, even this very thorough analysis of the possible effects of the observed mutations on protein structures, do not analyze any relevant disease phenotypic data.  The Bedford lab at least examined the rate of spread. These questions are better addressed using infection experiments with animals. If we want to know if there are changes in the symptoms, we should examined the progression of the disease in monkeys with serially times autopsies to see the order in which tissues show inflammation and signs of hemorrhaging for the 1976, 1995 and the 2014 viruses.

[Addendum 7/7/2015: Concern over the phenotypic differences in the 2014 Ebolavirus has penetrated higher levels of organizations like the CDC and the NIAID where descriptions now include statements such as “we understand most of the phenotype”. My own, and others’ expressed concerns over the effects of individual substitutions on the accuracy of PCR and immunohistochemistry-based diagnostic assays was and perhaps still is well-founded. A study published this month (Chambers et al., 2015) showed that a single mutation in the H3N2 influenza virus was responsible for the antigen drift that caused the relative inefficacy of the flu shot in 2014 (around 50% effective), which sickened as many as 1,700 in the US (Subtype A).

References

Carroll MW et al. 2015. Temporal and spatial analysis of the 2014–2015 Ebola virus outbreak in West AfricaNature, doi:10.1038/nature14594.

Chambers BS et al. 2015. Identification of Hemagglutinin Residues Responsible for H3N2 Antigenic Drift during the 2014-2015 Influenza Season. Cell Rep.  pii: S2211-1247(15)00588-4. doi: 10.1016/j.celrep.2015.06.005.

Gire, S.K., et al. 2014. Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak.Science 345, 1369–1372.

Olabode AS et al., 2015. Ebolavirus is evolving but not changing: No evidence for functional change in EBOV from 1976 to the 2014 outbreak. Virology. 482:202-7. doi: 10.1016/j.virol.2015.03.029.

Park et al., DJ  2015. Ebola virus epidemiology, transmission, and evolution during seven months in Sierra Leone. Cell doi:10.1016/j.cell.2015.06.007.

Faith, Fear, Reason, Science, Belief, Dogma and Infectious Disease Policies on Ebola

Faith, Fear, Reason, Science, Belief, Dogma and Infectious Disease Policies on Ebola

EVERY DAY we learn that the situation in Sierra Leone is worsening.  It’s been six weeks of large numbers of new cases of Ebola.  People who had hoped that we could see elimination are slowly realizing the sober truth: there risk of Ebola becoming endemic in the population is increasing.  This outcome would be provide a constant risk of a pandemic.

Evolution_is_RealAs an evolutionary biologist in a religious world, I recognize now, much the same as did eight months ago, an urgent need to share objective information about Ebolavirus.  I am an ardent defender of science as a way of knowing, but I do not participate in the anti-religious fervor that grips some of the atheist/agnostic community in the US.  In my view, one cannot say that they hold dear the Constitution of the United States, and eschew freedoms of religion at the same time.  The value of the expression of one’s faith is not only guaranteed by the Constitution, but it is held sacrosanct.

Reconciling science and religion is likely to be found a fruitless endeavor; as any good scientist knows, there is a demarcation between the knowable and unknowable; the testable and untestable.  Religion makes knowledge claims that cannot, and will not, ever be tested by science.  On such issues not only should science be mute; the formal logic of science provides zero information on whether any particular deity might exist.

As I studied the Ebola crisis, in performing research and interviews for the book, I became a student of humanity.  The total sum of the history of how the outbreak became an epidemic involved a convoluted and contorted mess of logic knots and inputs from every walk of life.  At the center of the epidemic, time and time again, I found humanity struggling to fill the void of ignorance about Ebola with a balance of science, reason, evidence, and rational thinking.  I also saw humanity attempt to fill in the blanks with fear, belief, emotion, and faith.   Somehow, these factors all had to interact to make public policy, and to cause people to act in specific ways consistent with shutting down the spread of the disease.  I saw people at both ends of the cognitive spectrum act in ways that reveal their dogmatic positions.  I found strength and compassion at both ends, and I found people using guilt, shame, post-hoc rationalization, and dogma to justify their position.

Public health policy decisions must be made in real time.  We have not been able to sorted out the differences among the various forms of religion over the last 4,000 years.  Policy decisions cannot wait: at times when data are lacking, they must be made with incomplete evidence.    I found that some of the public health policy statements and positions made thus far in the Ebola crisis lacking in terms of logical rigor.  I also found, time and again, zealots willing to look past the fact, for the sake of pushing a particular agenda, seemingly at all costs, sacrificing reason and science for the sake of influence over policy.  Scientists have their dogma, too.

Time and againthat I witnessed dangerous ignorance amplified by incorrect public statements about the nature of the virus, I found religious dogma at the center, making things worse.  People in some countries in Western Africa are not even taught the germ theory of disease: they had to be educated by the “Ebola is Real” campaign.  Many times, their minds would fill in the blanks where existing knowledge could be very helpful to their own survival – and helpful in shutting down the spread of Ebola – with superstitious beliefs and theories of curses and witchcraft.  Today, we learned that the WHO may have delayed putting out the call for emergency help with the outbreak out of concern over appearing hostile to Muslims wishing to make their pilgrimage to Mecca in October.

At the height of the epidemic,  government officials in the US dogmatically chastised the press for asking about the likely of Ebola being “airborne”.  The book explores the issue of this question in some detail.  The logic of the statements that “there is no evidence that Ebola is airborne”, and whether it is good idea to rely on the absence of evidence, is given a thorough treatment. While “airborne” may be a misnomer, it’s really a matter of size.  The American Academy of Pediatrics recommends against the use of baby powder because of the risk of respiratory problems.  Talcum powder, at ten microns, is known to cause respiratory distress in some babies.  Ebola, at 970 nm (0.97 microns)  is ten times smaller.  One-hundred thirteen ebola viruses could be lined up, end to end, on the thin edge of a dollar bill.  Ebola is smaller than most other infectious agents that are known to be airborne; in fact, it is smaller that the flu virus.  Some have chastised others for daring the ask questions about transmission modes, and have resorted to ad hominum attacks.  It is never irrational to ask objective questions in science; it is, however, irrational to draw scientific conclusions in the absences of evidence.

Eventually, enough people died to convince most in Western Africa that Ebola is Real.  There are hold-outs; they certainly fear the truth.  But the stench of the decaying bodies and the thousands of orphans are no substitute for scientific knowledge.  Informing populations in areas where education is rare and ignorance reigns supreme, when done in a reactionary manner, is ineffective.  Ironically, progress could not be made in Guinea until the Imams were given the task of educating the faithful. The Imams’ positions in society as leaders, not their specific roles, made them key players in helping to bend the curve.  Sociologists and cultural anthropologists could have told us that.

I use the book to advocate for education about biological health risks between outbreaks.  And, I will practice what I preach. Along with copies of my book, I will be sending used textbooks on Evolution and related topics to three public libraries: one in Sierra Leone, Guinea, and one in Liberia.

NewCover1_5 inches high 300 DPI

Why Sierra Leone is Raging with Ebola Again

Why Sierra Leone is Raging with Ebola Again

IN THE LONG RUN, THE ONLY THING THAT REALLY MATTERS in countries with Ebola circulating in the population is shutting down transmission.  After a continuous drop in the number of new cases per week since November 2014, we have now witnessed, for the past six weeks, a rate of spread that exceeds that of a majority of previous outbreaks.

In January 2015, Sierra Leone eased travel restrictions, and In February 2015, Liberia lifted the curfew, and re-opened its borders to Sierra Leone.  According to experts, people are becoming complacent.  Unsafe burials are being resumed.  People are letting their guard down.  Cultural norms like handshaking and hugging are more commonplace.  Instead of heading to Ebola Treatment Units for isolated health care, people are heading to regular hospitals.

There are hotspots to the east and west of Freetown in Sierra Leone.  Unfortunately, the practice of sick people hiding, and cultural misunderstandings on the nature of the illness, including belief that the disease symptoms are a result of a curse or a demon, continues to allow the virus to spread.  This renewed wave came from fisherman returning from the sea, and sharing a community toilet.  They had initially sought aid from traditional healers.

Sierra Leone has over 12,000 orphans from the epidemic.  Throughout West Africa, the CDC moved into a new phase of contact tracing as their primary mode of defense.  The UK had declined involvement of the US Army, and it is uncertain as to whether formal restrictions such as curfews and cordoned off “Ebola Resilient Capacity Zones”, which when isolated could be designated “Ebola Free Zones”.   This tactic has proven successful in other outbreaks such as the H1N5 influenza outbreaks in Egypt, Indonesia and Vietnam: it’s just easier to manage smaller, isolated geographic sections.  You can read more about this approach, and how policy decisions influence transmission risks in “Ebola: An Evolving Story” (World Press, 2015).

Hopefully the international community with step up their response and involvement.  Canada ceased their recruitment of new health care workers to help in Sierra Leone in early March.

With the uptick in cases, US pharmaceutical companies testing vaccines and treatments may have larger numbers of patients to enroll in their ongoing clinical trials.

Ebola: An Evolving Story (World Scientific)

Ebola: An Evolving Story (World Scientific)

Today, Liberia announced that it has released what appears to be their last EVD patient, a 58-year old teacher named Beatrice Yardolo.  This is a good sign, no, a great sign if it’s true… but that’s the catch.  The question now of Ebola is whether it will become endemic in the human population in West Africa.  I personally don’t think it will become part of the normal daily existence, but it is a virus.  It does evolve.  Right now the task is to track down all of the contacts via contact tracing.  That, along with the ending the practice of bring suspected cases to hospitals, seems to have helped turn the tide. For now.  Upticks in the number of new cases per week in Sierra Leone are troubliing.

Today I also received an updated look at the cover of the book from World.  It’s been less two months since I contacted World Scientific, and they have been doing all they can do to get the copy editing done as fast as possible.   The number of new cases per week peaked in September 2014 (at least we hope that’s the is highest we’ll see with this outbreak).  Let’s hope that they trend down again and stay down for 4-5 weeks more.

Naturally, I have mixed feelings about the book.  I wrote it because of the confusing mess of information in the press, in the testimony on the hill, mixed messages from experts.  The need for a clear, logical analysis was clear to me (and to many of my colleagues), and, thankfully to World Scientific.  They were the second publisher I approached with the book concept.  My editor replied with a simple “Yes, we will publish your book”.  World Scientific has been excellent to work with.

The mixed feelings come from my seemingly eternal position in life of dealing with the pain of loss due to death.  Every page of the book was written with the lost in mind, and their surviving loved ones, especially the orphaned children.  No one should have to try to make it in life without their own mom and dad.  Hopefully my colleagues will see the deep compassion and respect for everyone involved I felt for all involved, including the public, the scientists, the policy makers, and the politicians, whom I hope will digest and take to heart one of the messages of Ebola: that fear is not always a bad thing, sometimes it is necessary, and, odds are, it exists because it helped our ancestors survive in the face of danger.  It is important to keep in mind the difference between decisions made from fear expressed in an overly reactionary, emotional manner out of fear “which some call terror”, and decisions made from fear based on rational knowledge of the high risks of injury and death, which some call “respect”.

I’m fairly happy with the book as a window for the general public to see into the world of science and public health policy.  As confusing as the initial reaction to the outbreak and epidemic was, It seems to have provided a springboard of sorts into a new area of analysis of how we do research, how medicine is practiced, and how policy is (or, frequently) is not based on the most solid and best results of science.   Even before I finished Ebola, I found a new book forming on the side on the relationships between research, medical practice and public policy.  World is mulling over the second book.  I’ve completed a few chapters, but they will have to wait.  I have some galley proofs to review, and I have to get back to them on the cover.

Thinking of Liberia today, a boost in morale.

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