Coronavirus Origins: Anatomy of a Scientific Inference

Coronavirus Origins: Anatomy of a Scientific Inference

James Lyons-Weiler, PhD – 2/15/2020

Objective science is not about being right or wrong. It’s about positioning yourself toward maximizing your chances of learning something. Here I provide a lesson in the philosophy of Science – outlining an approach that, once abandoned, all of Science should strive to return.

THE PAST TWO WEEKS have been a fascinating exercise in Science – with many factors and forces influencing comprehension and expectation. I think it’s a fantastic opportunity for the public to have witnessed objective Science in action, and to see the definition of rigor in Science defined as operating in vacuum separated from profit motive and independent of ego.

The scientific philosopher Karl Popper urged scientists to move beyond the collection of pieces of information that confirm their favorite ideas. This type of inference-making is called positivism – and it leads to a bunch of collected facts and figures from an otherwise jumbled mess which, while appearing to be internally consistent and mutually supportive, can nevertheless be positively misleading to an incorrect inference. If we base our generalization from individual instances to the general case, a process called induction.

Since we base what we know about our world on observations, what could save us from merely agreeing with our Royal Selves with all of the confirming instances we can manage, or choose, to collect? And what do we do about the annoying contradicting observations that do not fit our induced generalized claims, since we have based our world view on all of the past confirming instances?

In other words, where does the demarcation exist between making stuff up and Science?

Enter: The Hypothesis

Popper offered a highly formalized calculus of the nature of objective scientific inference in which our goal should not be generalization via induction, but, instead, inferences more securely based on a form of deduction, specifically hypothetico-deductivism. In hypothetico-deductive science, we pose an hypothesis, or a conjecture, based on our Background Knowledge of a topic. At this time, we do not create a knowledge claim, upon which we stake our fame and glory (ego). Instead, we state the hypothesis clearly, and then imagine the most significant critical test of said hypothesis. For Popper, a Test is only truly critical if it can, in fact, potentially refute, or falsify, the stated hypothesis. If a Test does not truly place a hypothesis at the risk of being falsified, it’s not truly a critical test.

Enter: The Evidence

Once the Critical Test has been defined, and the scientific experiment or study has been executed, the information on the outcome of the Critical Test is called Evidence. We are to use, Popper says, the Evidence we have collected to re-assess the original Hypothesis, which you will recall was based on background knowledge.

If the critical test provides evidence that refutes the hypothesis, the hypothesis is considered falsified.

If the critical test provides evidence that fails to refute the hypothesis, and, importantly, the critical test was constructed and executed in such a manner that the hypothesis could actually be refuted if it were false, the hypothesis is said to be corroborated.

In either outcome, we update our background knowledge based on the evidence from the critical test, and move along secure in the hope that we have learned something.

Via H-D science, there is no role for ego; for Popper, the source of the hypothesis plays no necessary or useful role in whether the hypothesis will be falsified or not; i.e., the critical test is to be defined and constructed in a manner by which its design and execution is truly independent of whether the subjective scientist individually favors, or the current consensus favors, or dislikes, the hypothesis being tested. The only thing that matters is that the critical test is actually capable of potentially falsifying the hypothesis. That’s it.

If there was one word that should be dropped from discussions in science, it’s “prove”. Scientists don’t prove anything; as I say in discussions, proofs are for maths, logic, publications, and whiskey. Another term that I find to be extremely unscientific is “debunk”. The origin of the term has it roots in the term “bunkum”, of which the first recorded use was in 1828, when it was used to describe a “speech for Buncombe County, North Carolina” given by North Carolina representative Felix Walker during the 16th United States Congress (1819–1821). To “debunk” then means” to call someone out for bad, incorrect, or ineffectual speech, and if Science is being conducted objectively, it’s about the process, not about the speech, nor the speaker.

These terms are convenient clubs used by those who would gladly destroy the career of objective scientists whose results threaten their promise to their investors, and they play no role in the logic of Science.

Instead of these pop-culture representations of sciency-sounding things, it is importantly, that it is understood and expected that the available background knowledge, or assumptions, may not be perfect for any such enterprise in Science. In fact, the entire purpose of Evidence from a Critical Test is to determine whether the available background knowledge is to be updated, or left alone intact, unfettered by new knowledge. This is a far cry from “proving” an hypothesis. We simple either refute or fail to refute – and we only can do so if the test we use is, in fact, a critical test.

Bold vs. Weak Hypotheses

Popper did distinguish between weak hypotheses that do not go too far beyond the Background Knowledge and bold hypotheses that do go far beyond the background. These differences were important, because the further away from the background knowledge a stated hypothesis lays, the greater the degree of Corroboration – not confirmation, Corroboration – the Evidence from the Test results provide the hypothesis.

In fact, the more unexpected it is that the hypothesis survive a truly critical test, the more scientist should be impressed. Popper offered a term for this: Surprise. The higher the degree of surprise, the more improbable the outcome if the hypothesis was incorrect, and thus the higher the degree of corroboration – and the more we realize we need to update our background knowledge. Elegant.

Imagine if I come to you with a coin. I ask you: what do you think the chances are, if I flip this coin, you’d see it land on “Heads”. Most would say “50%” – a few would say “50%, if it’s ‘fair’ coin”. You watch me flip a coin, and it lands on its edge. This is so utterly improbable that you would not only be surprised: you’d be amazed. Now imagine if I give you the same coin, and you flip it – and it lands on its edge AGAIN. Clearly, you’d have found that the probability model in your head: 49.99999% chance heads, 49.99999% tails, 0.00002% edge, was wrong. You might flip it again, and again to determine how far off your 50:50:0 model was, and, for that coin, you’d say “Ok, this coin is not fair, it’s different” – if the data supported that.

Would you then generalize to all coins, and say “all coins are 10:10:80?”. No. That induction is not warranted from your observations with a single coin. That’s why independent replication is so important to Science- it determines whether an inference generalizes, and if so, how well it generalizes.

Entities that make overgeneralized claims often can get away with doing so because they carry the mantle of authority. But authority will not make a study replicate, or make a model able to predict well on new data. Biases from fraud, to hide evidence of harm from pharmaceutical and agricultural practices, are everywhere. In academia, to say so is death to one’s career. Which is why we need independent Scientists doing Objective Science in full view of the public. If it looks different, it’s because there is no agenda. I’m quite happy to be “wrong” over and over and over, as long as I am learning something about the world and the universe around us.

In the case of Coronavirus, the New Media and even some MSM picked up the idea that my statement that “at the present time, the most likely hypothesis is that novel coronavirus is lab-based” ignored the explicit caveat that Del Bigtree of The Highwire provide numerous times: it’s a ‘theory’ he said (he meant hypothesis). My infamous article actually listed multiple hypotheses, and presented the available evidenced structured as it was presented to me. I stated these hypotheses with every intent to attempt to define critical tests, old-school, in the Popperian fashion, to attempt to refute and thereby either falsify or corroborate each one. The last man standing wins.

This is only possible in a free and open society in which free and open discussions are possible. Numerous scientists from around the world have contacted me throughout the process to weigh in

It is no coincidence that Popper co-authored one of my favorite books: “The Open Society and Its Enemies” – highly recommended reading and something all who want open social media – freedom of expression – freedom of the press – freedom of Science from profit motive bias should read and give to their loved ones and friends.

Popper worked all of this out in formal calculus that, unfortunately, has all been but forgotten due to a non-sequitur “next phase” of the philosophy of science – Thomas Kuhn’s “Scientific Revolutions”, which focused on paradigm shifts, placing the power to create knowledge in the firm grasp of consensus – which of course we now know lends itself well to group think, to manipulations of perception, to propaganda, such as to claims of observational studies – weak science not capable of testing a core feature of important hypothesis of causality – as “rigorous” and sometimes even “more rigorous” than randomized prospective clinical trials with inert placebos. Under Popperian Science, the truth is reality, independent of us. It impacts us, it is something we approach asymptotically, using Science is a way of discovering knowledge. Under Kuhnian science, the loudest person in the room can define the truth; that often can mean the buyer with the largest purse.

Since entering into the domain of Coronavirus research, asking questions, posing hypotheses, defining critical tests, examining the evidence, and updating background knowledge based on the outcome of those tests, dozens of scientists from around the world have written to me in support of my efforts to address the questions we all have head-on. Some have been supportive, offering agreement; some have been supportive by challenging me. In reality, they were not challenging me, they were challenging the hypothesis. So I’m honestly grateful!

The manuscript showing the results of our study of spike protein motifs is under review, and I have asked the journal Editor to permit pre-review publication for the sake of humanity. If the publisher agrees, the results will be available to all very soon. Fingers crossed.

The conduct of independent science for the sake of knowing, in hopes it might reduce human pain and suffering, is gratifying because those who understand that it’s not about me – it’s about the 67,000 human beings with COVID-19 who may be suffering needlessly for want of a full understanding of the mechanisms of pathophysiology that SARS 2 has in it attack on humanity. It’s different from SARS – and understanding those difference draws on ecology, evolution, genetics, biochemistry, and an ability to divorce one’s ego or agenda from the outcomes of a study.

Posing incorrect hypotheses is a good, healthy and essential part of Science. Being willing to pose risky hypotheses is key to being able to make advances in knowledge.

Today, I received a card in the mail from a concerned US citizen who understands why IPAK exists, why independent Science must be made to thrive and grow in the face of a massive paradigm of science-for-the-stakeholders.

His card read:


If another planet offers you another position with bette(r) working conditions – free from politicized science, don’t take it!

We need you here.


This person’s enclosed donation to IPAK will keep objective, unbiased, but imperfect hypothetico-deductive Science alive in the US.

I feel that I have a responsibility at this time in history to reverse course on the tyranny of pseudoscience and Science-like activities conducted by individuals with an agenda other than using Science as a way of knowing.



Step 1: Background knowledge. No one could ID the novel segment. There had been 5 coronavirus outbreaks in China in seven years; 4 from the lab, 1 from a civet (cat-like animal) as an intermediate host. Vaccines made using recombined SARS spike proteins have been made and have undergone testing since the mid-2000’s.

Step 2: Initial observations. I found it to match p-ShuttleSN, which was clearly related (somehow) to the Coronavirus Spike protein. Found a patent for a SARS vaccine that used pShuttle-SN to move a SARS spike protein into an adenovirus.

Step 3: I made the bold conjecture, given the background knowledge of a 4:1 risk of accidental vs. laboratory release of SARS coronavirus, that this was (a) likely an accidental laboratory release, and (b) most likely of laboratory origin


I used phylogenetics to determine the relationship of all of the Spike protein sequences I could access, including pShuttle-SN. I sought new evidence: If pShuttle-SN turned out to be most closely related to SARS CoV 2, it may well be related causally.

It wasn’t. It clustered with SARS CoV-1, specifically, in what I call the “Cancer Center cluster”, with sequences from a Genome Center. While it was possible to replicate the alignment issue with other coronaviruses, it seemed to be related to a shorted N-terminal Domain of the S1 section of the Spike protein. Noted.

Further test: Other artificially modified spike proteins might be most closely related to SARS CoV 2.

They aren’t.

A final critical test: Since SARS CoV Spike protein is different, and different because it was from nature, but, were there any reliable sequences from a natural source from long ago that had the same type of Spike protein? If so, then we have to rule out laboratory ORIGIN – as in design, because such as finding would be highly improbable.

Result: Using motifs, I searched known B-Coronavirus Spike proteins to see if there were any older sequences from nature that also include the motif pattern that appears to be indicate (may be) indicative of a the special pathogenicity in SARS CoV 2. I found one that matched all of the known closest relatives and examples of SARS CoV 2. It was from 2005 and from a natural source: a bat. (Details to appear soon following peer-review or agreement to pre-publish).

The net result? We have updated our background knowledge, and learned something new. We have a potentially useful pathogenicity signal (shorted NTD, two missing motifs and a Gp40 motif in the C-terminal region) that anyone with a high school degree could learn to recognize with about 20 minutes training, a laptop and access to the internet. The new hypothesis – that a pathogenicity signal exists – itself is a conjecture, and needs to be tested. It falls into the realm of “Applied Science”, drawn from “Pure Science” – the act of daring to ask questions and pose hypotheses merely for the sake of knowing.

So there we have it – the Anatomy of a Scientific Inference. In my view, all of Science should return to Popperian Hypothetico-Deductivism and cast off the control of the funding masters who limit what we can study, and what we can publish. Remember that to do Objective Science means divorcing your ego from your hypothesis.

Some will complain in the comments that the Philosophy of Science has ‘moved’ on, but in reality, I’m not accepting that. Kuhn’s permission slip for induction – and that’s what it has been used for – has led biological sciences and medical sciences down a path that is making people sick. Philosophers of Science who used to enjoin Popper have abandoned all hope in the face of the juggernaut and have become Stoics – a metaphysical rising above the issues as irreconcilable. Two decades ago, I proved (using logic), using Popper’s calculus that having more scientists looking at the same problem and discussing it is more likely to yield progress in science – simple because each had their own background knowledge, meaning that the chances that someone in the room has the missing component of background knowledge to accurately and correctly interpret the evidence of a critical test of a hypothesis. The journal editor returned the manuscript with the apology that no one uses Popper’s calculus anymore. That needs to change.

Nevertheless, Vestiges of Objective Science still exist: We still use experiments with controls to test the hypothesis of interest – and the degree to which we can reject the null hypothesis is measured by a p-value. That p-value is the degree of surprise that we should express if we saw the null hypothesis rejected by chance alone. Like flipping a coin and seeing it land on its edge. We know there is a small probability, and if it were to happen again and again, we would have to surmise that our background knowledge, or expectation, needed to be updated.

But if we cannot discuss hypotheses for fear of being ‘wrong’, or cannot publish results because it may upset our funding source, or it may go against any particular political agenda, we’re going down the wrong path. We still don’t know if there is something different in China with respect to the mortality rate of the novel coronavirus. The two hypotheses that I posed

(A) the Chinese government proceeded with a large-scale coronavirus vaccination trial, or

(B) the new vaccine law (Dec 1, 2019) may be related somehow

will both soon be partly tested by the amount of of serious illness and death outside of China associated with infection. So far, there have been only four deaths outside of China, in 688 known cases, a rate of 0.005% (about what I predicted). In China, the per-case fatality rate estimate ranges from 2.1% to 2.3%, depending on whether suspected cases are included in the denominator of the total number of cases. Hopefully for the world, this hypothesis bears out.

Science is a social enterprise by which we compare our interpretations of outcomes of studies with other scientists, who can share theirs back. The age of “retraction” due to differences in interpretation, and “debunking” by shady characters with ties to Pharmaceutical companies, are over. I’ve led chants of “What do you want?” to which the crowd replies “SCIENCE!” and I have to tell you, I think we’ve reached a turning point where profitability is being given the boot out of the logical calculus of Science, and the public is learning the difference between Science, and Science-Like Activities.

I encourage every Scientist to state their bold hypotheses loudly, and clearly, and outline their reasoning. Because, as my Master’s degree mentor Paul Colinvaux shared with me, his academic advisor Dan Livingstone thought that being found to have posed an incorrect hypothesis would be “wonderful, because then we would have learned something”.

SARS CoV-2 CASES TO DATE (2/14/2020)– Update here.

Mainland China: 63,862
Thailand: 33
Japan: 29 (plus more than 200 on cruise ship off coast)
Singapore: 67
Hong Kong: 56
South Korea: 28
Taiwan: 18
Australia: 15
Malaysia: 19
Germany: 16
Vietnam: 16
Macau: 10
U.S.: 15
France: 11
United Arab Emirates: 8
Canada: 7
Italy: 3
Russia: 2
UK: 9
Philippines: 3
Cambodia: 1
India: 3
Belgium: 1
Finland: 1
Nepal: 1
Spain: 2
Sri Lanka: 1
Sweden: 1

Why Popper Was Right About Induction – And Why It Will Always Matter


THE PHILOSOPHY OF SCIENCE is to many a collection of old thoughts in dusty books and journals, logical meanderings and debates about semantic definitions. It would appear that to the majority of philosophers of science (those left) who have not abandoned all hope and left for stoicism that schools of thought based on induction are reasonable, or, at least the best we can do.

The problem began when humankind began wondering: are we rational beings?  Do we reason differently from animals, and, if so, what are the fundamental aspects of human reasoning that would allow us to call ourselves rationale beings?   Popper clearly disallowed even the existence of induction, ending the need for the question on whether induction is rationale, ending, it would seem, the problem best posed by David Hume:

  1. We reason, and must reason, inductively;
  2. Inductive reasoning is invalid;
  3. To reason in a logically invalid way is irrational.

Therefore, we must be irrational.

Hume’s ideas drive us to compare inductive reasoning and deductive reasoning, and Popper’s hypothetico-deductivism and critical rationalism inverts the problems of irrational generalization into a framework of logic that, like pure induction, makes predictions, but, unlike induction, reserves knowledge as that which has survive repeated attempts at falsification.  Popper’s solution to the irrationality of induction was to conclude that induction does not exist, which led his critics to search his hypothetico-deductivism for evidence of induction smuggled in somehow.

Some thought Popper evaded Hume.  Popper said people who think that do not truly understand his formal calculus of logic.  Having read most of what Popper wrote, and considering the proposed alternatives, all of which propose to return science to inductive reasoning, I think it is worth reviewing why those who say that philosophers of science have “moved on” from Popper may be correct, but they are wrong in thinking that Science can benefit in any way by adopting any inductive inference framework in lieu of hypothetico-deductivism.

First, let’s look at Popper.

Given Background Knowledge B, generate Hypothesis H. Think of the most critical test (T) that could falsify H.  Conduct T to gather Evidence (E).  Interpret H in light of E given B.  Update H, and/or B, as necessary.

Now, let’s look at “Inference to the Best Explanation”, or IBE, which some take as an inductive alternative to Popperian Hypothetic-Deductive Reasoning.

Observe phenomenon P. Think of all of the hypotheses H1, H2, H3… Hn that might explain P.  Consider lines of evidence that can rule out various Hi’s.  Any Hi’s that remain are more probably true because they “best explain” P.

IBE is considered to use induction. But does it?  It is really different from H-D?  Let’s see:

The Phenomenon P requires and explanation.  “The Butler Did It” is one explanation, but it is also an hypothesis H.  To test hypothesis H, we try to find reasons (evidence) that can rule it out.  How do we find evidence?  We conduct a test of some kind, which leads to more observation…. did the Butler have a motive, opportunity and means?  Three tests (T1, T2, T3) just one H, but still tests.  If the Butler had motive, but not opportunity nor means (say, he was in Hawaii) – well, we can consider the hypothesis “The Butler Did It” falsified.  We can estimate the probability of being true as very small.

  • In the IBE, the focus has always been on the probability that the most likely and most simple hypothesis explains the data.  This makes sense because we all have our own experience in understanding following explanations.  However, it does not mean that induction is employed.  In fact, a series of T’s to test a series of H to provide a series of E, all interpreted in the context of accepted B is still Popperian logic.

For Popper, induction simply did not even exist.  And I agree.  What he meant was that valid knowledge claims made from rational inference never involve induction.  We call use induction all the time; we generalize, for example, from our experience that we cannot walk on water – any water.  But if you’ve never seen a frozen pond or a lake, well that’s a different story.  That’s the risk of induction – it can always be wrong up to the point until we have collected, observed, measured, witnessed every last instance and proven the generalization correct.  At the very moment when we collect the last observation… induction disappears, because we have the entire set, and we then can safely make our deductive inference, whatever that may be.

The departures from Popper with dalliances with induction have untethered the philosophy of science, and science itself, to a period of irrationality that has arguably facilitated a no-holds barred wrestling match with, and for, very different versions of reality in various domains of inquiry.  Partly creating and filling the void first was Kuhn, whose revolutions in science depended heavily on consensus to define knowledge.  Of course now, that looks a bit like a popularity contest, and rational thought tells us that so many pieces of information held in esteem as correct by so many (scientific or medical) minds does not actually measure whether those bits of information are, in fact, true; surely there are more rational ways to understand what science is, and how science works than to allow the loudest (or best funded) 800-pound gorilla in the room to carry the day.

Kuhn’s popularity contest encouraged the development of the Skeptics movement, in which public ridicule became an enforcer of reality.  Individuals who held notions, ideas, questions, theories or even hypotheses that had been “debunked” were once and forevermore, in the minds of the Skeptics at least, PROVEN wrong, which requires a very strong, positivist induction about absolute truth, which, for me and for many critical rationalists, is unscientific.  Science always leaves the door open that what may be a prevailing view today may be found to be incorrect, to a degree or in whole, tomorrow, and while Skeptics say this, in the application of the intentionally pejorative label “debunked”, the Skeptic is playing with inductive fire, because their determination is meant to be definitive, a positive knowledge claim, a universal truth.  In reality, of course, they can be wrong on their view that a particular idea has been “debunked”.

Others, notably Musgrave (2004), have analyzed whether, and how, Popper may have slipped up and allowed induction into his logic of science.  Musgrave cleverly put the smuggling of induction back on those who accused Popper of using induction and comes very close I think to giving the Popperian framework more than a fighting chance to be taken seriously.  However, in a world in which prevailing views are considered valuable, and in which billions of dollars of capital depend on the public – and the scientific and medical community – to accept a particular version of reality, there is little incentive to non-purists to accept or even anticipate a revival of Popperian philosophy.

We must admit, though, that Popper’s main goal was not prescriptive, but was, rather, a description of what science is, and how it is conducted.  Scientists even today rely on hypotheses; to dispense with the hypothesis is to cut out the scientist.  Companies with products could dispense with the entire charade of Science-like activities and merely publish knowledge claims that go beyond the available evidence – the best headlines money can buy.  No, the hypothesis is not dead.  Tests of hypotheses – and the attempt to falsify them (in the null form) are ubiquitous among published scientific studies.  There are some who lament the over-reliance on the p-value, and its misinterpretation, but certainly the probability that a null hypothesis might be found to be incorrect incorrectly by chance is still relevant.  The social aspects of the science as an enterprise – communicating results to peers, interpreting results – can either be seen as an opportunity to attempt to sway prevailing views, or as a responsible reality check against subjective or parochial restrictions.  The opportunist, or hack, would prefer the former; the purist the latter.

Popper should be celebrated as a master of the caveats, with expressions that are sometimes missed such as “for the time being”, and “as far as one can tell” and even his concept of Conjectural Knowledge – but he also bedeviled his readers with inconsistent claims that words (semantics) do not matter, that new terminology should be tolerated, and that his critics did not fully understand him.  All of these rallied thinkers to examine for themselves logic and thought processes in a new light, to question the definition of the word ‘belief’ (which Popper famously claimed to not believe in).  So, what was Popper up to?  Why did he claim that subjective belief played no role – zero – in what he understood as Science?

Popper sought to solve the problem of Demarcation – that is, having a category system in which activities that actually qualified as science could be placed into a bin labeled “Science”, and that other activities could be placed into another bin labeled “Not Science”.  It was critical for Popper that Science be rational, that is, as a process, science did not dissolve into what is called the infinite regression, in which peeling back layers of knowledge reveals that each layer is based fundamentally on previous unfounded (irrational) generalizations because they, themselves, were based on inductive reasoning.

A classic description of inductive as generalization used by Popper was the knowledge claim that “All Swans Are White”.  The set-up is that if a person has only ever seen White Swans, their experience tells them only that white swans exist.   A claim that “All Swans Are White” is inductive inference that goes beyond their experience (beyond the evidence available to them).  The claim is clearly not supported by past experience alone, because it involves Swans not yet seen.

For Popper, science progresses beyond induction if one makes a conjecture that is then intentionally subject to refutation by some critical test.  A conjecture is an operational claim, not meant to be applied as workable model of reality, that, when subjected to a critical test, is either falsified, or it survives the test.  The survival of the test does not confirm the claim; that for Popper was too strong a word; instead, the surviving hypothesis is corroborated, and it acquires a feature he called verisimilitude (meaning closeness or approaching Truth).  In Popperian Science, truth is never claimed, beliefs play no role, and induction, if it exist, only exists for a brief, transitive operational form – think tongue-in-cheek – not for the purpose of a knowledge claim, but, instead, in the form of a working hypothesis – something far short of a knowledge claim – that can, in principle, be cut down by evidence from a test, interpreted in light of background knowledge.

The reason why induction does not exist is clear from the Swan example: In hypothetico-deductivism, the claim that all swans are white can be falsified by finding just one black swan.   In induction, one can attempt to confirm the claim by pointing to all the white swans one has seen.  Finding more and more white swans, however, never confirms the claim, because there may be, hidden somewhere, a lone, black swan.  The only solution to truly test the claim is to collect all swans in the world and check their color. When the last swan is collected, at that very point, the inferential exercise flips from inductive to deductive.  Induction, it would seem, does indeed not exist (as a form of rational inquiry).

This is why induction does not exist.  Generalizations themselves are, by the nature of their existence, eternally subject to being falsified by new observations.

Why This Matters

In the marketplace of ideas, the ideas of science-based or evidence-based medicine carry a lot of gravitas – they appeal to the desire for comfort of knowledge that medical procedures, drugs, and biologics used on patients are being used rationally, that is with a basis found on objective Science.  The public, however, has first-hand experience with an ever-shifting understanding of what Science is telling them.  Butter is unhealthy.  Now, eat butter.  Cholesterol is bad. Now it’s not so bad after all.  There is a fixed blood-brain-barrier.  Oops, no, there is not.

Let’s examine a prevailing view:

“Vaccines do not cause autism.”

Now I’ll inform you that “Wait, not all vaccines have been tested for association with autism”.

That should tell any logician that holding on to “VaccineS do not cause autism” requires use of arbitrary belief, placing it, if you’re Popperian, outside the realm of Science.

And if I inform you that “Association studies do not test hypotheses of causality”, and that “All studies on vaccines that have been examined have been association studies, not randomized blinded clinical trials”, then, if you’re Popperian, you see that the most critical test T has not been conducted.

And then consider that “Some studies do exist that have found higher risk of autism following vaccination” and that AAP and CDC’s lists fail to include such studies, if you’re Popperian, then you might say that AAP and CDC are not constructing a complete and unbiased Background Knowledge, or that they are ignoring the results of Tests which do not fit their arbitrary belief.

And consider “Scientists have for some time suspected that a genetically at-risk subset of individuals exist that have a higher risk of autism from vaccines than others”.

If you’re Popperian, then you might say “Fine, that’s a well-posed hypothesis. Let’s do the Science necessary to Test and attempt to falsify the hypothesis.”

If any of the last four statements are correct, no rational being could possibly conclude “All vaccines do not cause autism”.

But that is what the Kuhnian juggernaut of the CDC has the media telling you. And what likely 99% of all medical professionals will tell you, all the while stating that there have been dozens, hundreds, or maybe thousands of studies that show that vaccines do not cause autism.

They don’t know how many studies.  They’ve not read the studies.

Either all of these individuals are misled, are misleading, or have some justification.

At the root of the use of unwarranted generalizations, and willful ignorance of evidence that falsifies those generalizations is a fear – a fear that the public will stop accepting vaccines – if they are informed of the realities of vaccine risk.  Fear is irrationality – and the inaction by those who decided to stick our collective heads in the sand for over 15 years tells us that they are… not Scientists.

HHS’s Unfulfilled Duties

It is not exactly clear who decided that HHS would not fulfill the Congressional mandates made in 1986 to make vaccines safer, and to find ways to identify those at highest risk.  But HHS never even attempted those tasks.  Instead, they undertook (via the CDC and contractees) science-like activities designed to manipulate and control public perception.  From 1986 to the present, CDC pushed out studies that found, repeated, no association between vaccination (mostly with MMR) and autism.  Not all vaccines have been tested, though, and some studies conducted by others have, in fact found association.  Positive results are dismissed, however, because association falls shy of testing causality.  And that is precisely where we stand today, and have stood, since the last Institute of Medicine report that made the inductive leap from “vaccines studied” to “vaccines”.

But HHS has a special responsibility in this debacle.  Congress mandated them in 1986 to make vaccines safer, and to find those most at risk from serious adverse events.  ICANN and Robert F. Kennedy, Jr. received an admission in court from HHS that they have never filed the required biennial report required of them by the 1986 National Childhood Vaccine Injury Act.  Instead, they labeled serious adverse events “moderate” on Vaccine Information Sheets.  They censored US citizens who participate in their open comment period when they considered weakening the MMR Vaccine Information Sheets because they might scare people away from using the MMR Vaccine. They have conducted cooked studies “to show” that vaccines do not cause autism – all association studies, most very, very poorly designed, off-target, underpowered and manipulated to provide evidence to support the claim

“Vaccines Do Not Cause Autism”.

Science does not put forward evidence to support a hypothesis, it tries to refute it.  The genetic x environment hypothesis has never been tested.

It’s time for a return to Science.

Let’s move forward with studies that are aimed at designing models that are shown empirically to detect with high accuracy those children or families who are highest risk of developing neurodevelopmental disorders from neuroimmunotoxins and genetics, and let’s make sure those predictive models are based on profoundly sound and logical hypothetico-deductive inferences.

Postscript: As for Hume, the answer is: Thanks, but it’s a trick question.  Humankind can be rational at some times (deductive), and irrational at other times (inductive).  Induction is where the risk lies, but knowledge, in the end, always comes from deduction.


Musgrave, A. 2004. How Popper [Might Have] Solved the Problem of Induction – Jstor