When it became clear that the corona event was going to get serious, I started looking into the science behind viral disease. Like most of us, I had been taught about germ theory in high school and hadn’t given it much thought since. What I had heard about, for example, new findings around our microbiome, made me suspicious of the official narrative that was taking shape around corona. However, given that it looked like we were about to shut our society down, I assumed there must have been some big breakthroughs in the science that had given us new certainty in relation to viruses.
I was right about the big breakthroughs in the science but wrong about the certainties. In fact, the scientific breakthroughs in microbiology of the last few decades have made the whole field far less certain and this uncertainty stands in direct contrast to our single-minded response to corona. In post 2 of this series, I made the claim that the corona event could never have happened without the PCR test. In this post, we’ll see that the PCR test and other technological advancements have completely upended the naive version of germ theory which has been the primary mode of explanation in the public discourse around corona and we’ll see that it’s not just germ theory that gets brought into question but our entire conception of selfhood.
Right from the start of the corona event, the focus has been all about ‘infection’. I began my investigations into the science by trying to find out how we tested for infections. I learned about the PCR technology and that it was a form of genetic detection. A virologist finds what they think is the virus causing the infection, they analyse its genome and come up with a segment of the genome that they think uniquely identifies just that virus and nothing else. The PCR test, an incredibly complex bit of technology involving all kinds of chemical processes and fluorescent probes, looks for that segment of genome. It is a calibrated test, which means that you have to find the right number of cycles for it to give the most accurate results. Like all biological tests, there will be an error rate and it is up to the technician and others to ensure the error rate is as low as possible. The error rate exists in the test itself (which chemicals are used etc), in the collection of the sample (contamination, invalid sample capture), and in the laboratory processing (technician error, temperature, contamination etc).
There are 99 potential problems with the PCR test and it seemed to me that you’d want some very strict quality control measures to ensure that the system as a whole was not producing excessive errors. In the rush to respond to corona, we actually threw those quality control measures overboard. We allowed ‘emergency approval’ of the test kits, bypassing the usual quality control measures. We heard stories of whole batches of test kits being invalid. In Melbourne, we had run out of qualified people to take samples so we had non-specialists going door-to-door to test people. We even had ‘self service’ test kits where people could sample themselves. And it seemed that nobody was testing the labs to ensure they were producing accurate results. In short, we had set up a system that seemed guaranteed to produce error. When the President of Tanzania produced his famous speech about test results coming back positive for various fruits and farm animals, those of us who knew how the system worked were not at all surprised.
Setting aside the logistical issues with the tests, the main problem from a theoretical point of view is that we were using the PCR test as the ‘gold standard’. In Australia, the government considered you to be a ‘confirmed’ case on the basis of a single positive test. This is a problem because the PCR test does not ‘prove’ causality. It is not a ‘gold standard’ test in the sense in which I understood the term. The gold standard test as I understood it was based on Koch’s postulates but it seemed that nobody had run that test. Until that had been done, how could you know that the PCR test was valid at all?
Opponents of the measures undertaken during the corona event were using this failure to fulfil Koch’s postulates to argue that our response was invalid. As it happens, most of the people I came across making that argument were also advocates of a little-known theory of disease called terrain theory. In listening to their objections to the PCR test, I also heard about their alternative take on what was happening. In our society, the terrain theory is supposedly discredited while the germ theory is the accepted and yet it seemed to me without looking into it further that modern microbiology had as much support for terrain theory as for germ theory. We will see exactly how much as we progress.
For now, let’s do a very quick summary of the two positions. Everybody knows germ theory as it is the default in our culture. A pathogenic germ comes from outside the body, gets inside and makes us sick. Louis Pasteur was one of the foremost exponents in his day and he had the idea that a single germ should cause a single illness. Robert Koch came up with his postulates as an attempt to put the germ theory, which at the time was not yet in the ascendant, on firm scientific footing.
Some version of the terrain theory was actually the default position of most scientists in the 19th century but the version that comes down to us today is mostly attributed to Antoine Bechamp. Leaving aside the specific mechanics of how it might happen, the theory states that illness comes first and then germs are attracted to the illness. That is, the body first becomes weakened and in that weakened state germs are able to gain a foothold.
Exponents of the terrain theory like to invoke Koch’s postulates because those postulates have never worked for viruses and for many other pathogens as well. Even in Koch’s day, it was known that the postulates did not apply across the board. Later there would be the technical problem that viruses cannot be propagated in pure culture which was a requirement of Koch’s third postulate. But more importantly there was the problem of asymptomatic cases and this is where the link to the corona event becomes clearest.
When I first heard about all the asymptomatic corona ‘cases’ my first impression was that it was great news. Here’s a virus that’s so weak that it doesn’t even make most people sick. Surely that was cause for celebration. The media response was the opposite. We heard horror stories about asymptomatic ‘carriers’ and how this was terrible because it meant that you couldn’t know who was spreading the virus from symptoms alone. This reveals a key pattern with corona event and one that driven both the public’s understanding and also the public health bureaucracy’s understanding. With the corona event, we have focused almost entirely on ‘infection’ and very little on ‘disease’. The strange thing about that is that it is a repetition of the very beginning of the germ theory vs terrain theory debate that was going on back when Pasteur and Koch and Bechamp were discussing the matter. The early opponents to germ theory pointed to asymptomatic cases as evidence against germ theory. The germ theorists pointed out that it was awful because it meant we had invisible carriers of a virus.
Let’s return to Koch’s postulates.
The germ theorists wanted to be able to prove a causal relation between a virus and an illness. But if you have asymptomatic cases, then there is no fixed causal relation. All you can say is that the virus ‘might’ cause illness. In fact, Koch had to make exactly this modification to his postulates. Where he wanted to say the virus ‘must’ cause illness he could only say it ‘may’ cause illness. This seemingly small alteration in language has been everywhere during the corona event. We have heard endlessly about what ‘could’ happen and what ‘might’ happen. These horror stories go right to the heart of the uncertainty caused by the fact that Koch’s postulates cannot be fulfilled. Terrain theorists point to this uncertainty as evidence that they are right. According to them, the difference between the asymptomatic person and the symptomatic one is the terrain: the person’s own body. The epidemiological evidence around corona provides justification for this. Statistically, the people who have gotten sick were overwhelming the elderly and immuno-compromised. The germ theory exponents fought back by highlighting stories of otherwise healthy people who got sick but these were rare individual cases many of which were found to be of dubious veracity.
The question of asymptomatic cases has thus been at the core of the germ theory vs terrain theory debate right from the start. That it should rear its head with the corona event is no surprise. There are all kinds of statistics floating around about the asymptomatic rate of sars-cov-2 infections. I’ve seen everything from 40%-80%. The fact that the public debate has turned what should be good news into cause for alarm is not a coincidence. It reveals that the germ theory interpretation has been foregrounded at the expense of the terrain theory.
This is no surprise. Our public health bureaucrats, through their counterparts in the WHO and other such bodies, chose a pandemic response strategy that implies a simplified version of the germ theory of disease. It is no coincidence that this strategy, like the naïve version of germ theory that it uses, is straight out of the 19th century. From the beginning of the lockdown and even before, there has been a political imperative to completely disallow public debate that could call the strategy into question. We will look at this issue in the last part of this post.
For now, let’s look at what modern microbiology has to tell us about viruses and viral illness. We will see that our public health response to the corona event is completely out of date with modern microbiology. Ironically, it is the very technology that we have used to detect infections – the PCR test – alongside other technological advances that has blown open the question of germ theory vs terrain theory.
The Microbiome and the Virome
The naïve version of germ theory, the one that is part of our collective cultural subconscious, is that our body is ourselves and the world is outside of us. The germs ‘live’ in the world outside and they try to get into our body where they cause trouble. This notion goes right back to Pasteur and Koch. The truth is this idea hasn’t corresponded to scientific understanding for many many decades. As far back as 1950s and probably earlier, we knew about chronic infections; viruses that exist in the body indefinitely. At that time, just as now, there was an explosion of technological advancement in the identification of viruses. That led, just as now, to all kinds of spurious correlations with vaguely defined illness. Huebner wrote in 1957:
In addition to many opportunities for spurious etiologic associations provided by the simple chance occurrence of numerous ubiquitous and prevalent viruses, some representatives of these agents are demonstrably persistent in the human host for weeks or months . . . and simultaneous multiple viral infections are extremely common.
In the last twenty or thirty years, we have seen a repeat of what happened back around the 1950s i.e. a huge explosion in viral identification due to technological breakthroughs. We have seen a repeat of the surge in spurious etiological associations calling into question once again the problem of Koch’s postulates. But this time, the technological breakthroughs are not just a problem for microbiology. This time we have a whole new paradigm shift in what we thought we knew about the human body. The PCR test and other gene-based tools of analysis have opened up a new world but this new world challenges not just the germ theory of disease but our entire conception of our self.
We now know that viruses are literally everywhere in the world. The oceans in particular are a melting pot of viruses but viruses are on land, in the air and all other places. It is said there are possibly 1031 viruses in the world. In every human body, there could be 380 trillion viruses.
Most people would have heard about the microbiome in particular in relation to gut health. It turns out each of us also has a virome and the virome appears to be larger than the microbiome. There are more viruses inside us than bacteria. They appear to be in all places on and inside us: our blood, our mouths, our gut, our skin. Those facts are hard enough to wrap your head around but it also turns out that a very large number of those viruses are from exogenous sources. That is, they originated in the outside world. Even in human blood, researchers have found all kinds of viruses, fungi and bacteria that originated outside the body which raises all kinds of questions of how they got there. Presumably it must be through the intestinal tract.
This is, of course, a huge problem for naive germ theory. We are not self-contained entities just minding our own business and waiting for a nasty virus to come along. We are more like an ecosystem of micro-organisms (including viruses) most of which are in a symbiotic relationship with us:
Perhaps the most radical change is the realization that most of the microbes that inhabit our body supply crucial ecosystem services that benefit the entire host-microbe system. These services include the production of important resources, bioconversion of nutrients, and protection against pathogenic microbes.” (Young, 2017)
That’s right: viruses can protect us from other pathogenic microbes. We are even now starting to research using viruses as a form of disease prevention or mitigation thus completely turning the germ theory of disease on its ear.
Of course, most of these viruses are bacteriophages and the like. What about the viruses that are typically associated with illness? Well, we already know from the corona event, that we can be infected by such viruses without getting sick but the research is only beginning to show how prevalent that is. During the corona event we still assumed that asymptomatic people had been newly infected but it’s starting to look like asymptomatic infection by potentially disease-causing viruses is the norm. Studies that test asymptomatic people for infection are relatively new but are showing that it is perfectly normal to be infected by a virus that could make you sick but doesn’t.
Although malaria, most Leptospira spp., influenza, and dengue were identified more frequently among the febrile [feverish] patients, the detection of these same pathogens in the afebrile control group at a nontrivial rate was striking…
We now know that potentially pathogenic viruses can be inside us without causing illness. We know we can have multiple infections of ostensibly pathogenic viruses at the same time. Another study found that you were more likely to get sick with a single infection than with multiple. Another study found that some viruses require coinfection to cause illness. This all raises the question: what is it that causes the illness. It can’t just be the virus. Maybe it is something in the terrain too?
All these new findings exacerbate the uncertainty that already existed around Koch’s postulates and causality of viral illness. We can’t assume there is a one to one relationship between a virus and an illness. This leads to all kinds of computational difficulties if you were to approach the matter in a purely statistical fashion. Furthermore, in order to get reliable statistics, you would need mass testing of the population to try and figure out how many asymptomatic infections are there. But that would be just the start of the problem because now you need to try and figure out which variable differentiates the asymptomatic from the symptomatic.
For example, let’s say we have 50% of people infected with sars-cov-2 who are asymptomatic. We want to know what is the difference between them and symptomatic people? It could be the presence of another virus. It could be the absence of another virus! It could be a general state of health or lifestyle matters or geographic factors like air pollution. How do you reduce the number of variables down to a manageable size?
That the PCR and other technological advancements have made these problems more pronounced is well known within mainstream microbiology:
As with traditional culture techniques, nucleic acid amplification technology has the ability to detect microbes that may behave as ‘‘true’’ or frequent pathogens, transient or permanent commensals, opportunists that take advantage of pre-existing pathology or altered host defences. The difficulty in making these distinctions is made more challenging by the extreme sensitivity of the amplification technology. (Fredricks and Relman, 1996)
It is one of history’s ironies that the corona event and the naïve interpretation of the germ theory implied by it should come at exactly the time that microbiology is showing how outdated that germ theory is. What’s more, all this new information is actually shifting the focus back towards the terrain theory as an explanatory framework because in an ecosystem perspective you can’t worry about simplistic cause and effect. There are too many variables to calculate to find cause and effect. You have to fall back to observation of the system as a whole and that is exactly what terrain theory implies. This observation of the system as a whole is exactly what epidemiology does. I mentioned in earlier posts how we relegated epidemiology in our response to corona and this has been a big mistake in my opinion.
There have been and still are ongoing attempts within microbiology to save the underlying notion of Koch’s postulates. One of the more recent ones is from Fredericks and Relman who suggested a new set of postulates that aimed to account for the technological advances of recent times and put microbiology on a more secure footing. Let’s look at just the first two of those postulates as they relate to the corona event:-
- A nucleic acid sequence belonging to a putative pathogen should be present in most cases of an infectious disease.
Straight off the bat we have a problem in relation to the corona event. As I pointed out in earlier posts, the disease ‘covid-19’ doesn’t have unique symptoms. Thus, it’s not clear what ‘disease’ means here. You can say the disease is covid-19 but the only way to know that is from the PCR test which leads to circularity. On the other hand, if you say the disease is pneumonia or Influenza Like Illness, then we still have a problem. In Australia, for example, the overall test positive rate last time I checked was about 0.5%. That is certainly not ‘most cases’ and would therefore fail this criterion.
- Fewer, or no, copy numbers of pathogen-associated nucleic acid sequences should occur in hosts or tissues without disease.
I read this to mean, the number of asymptomatic ‘cases’ should be less than symptomatic ones. As stated earlier, the asymptomatic rate for sars-cov-2 is said to be somewhere between 40%-80%. This would seem to be a negative on this criterion.
Based on what, in my opinion, are the two most important criteria of their list, I would say that sars-cov-2 does not cause covid-19. The problem is that Fredericks and Relman say that not all of their criteria need to be fulfilled and that there must be scientific ‘concordance’ on these matters. But where does that leave us except in a position that we have to trust the experts. The whole point of Koch’s postulates was to fix objective criteria by which these things could be discussed. Such criteria are also implied by the reproducibility criteria of science. If I can’t reproduce your work because we cannot agree on the interpretation of the rules then we can argue endlessly about semantics with no result.
Whilst I have no dog in the fight (at least I didn’t until the corona event), it seems to me that we have more than a hundred years now of germ theorists coming up with criteria that never get satisfied. At what point do we say the germ theory as a whole is on the wrong path?
There is an idea that seems prevalent in microbiology that all these new technologies are going to open up opportunities for new understanding. I see the exact opposite. There are going to be way too many variables to calculate. It’s going to be the three-body problem on steroids. False positives are going to be the norm even by researchers who are doing good work let alone sloppy speculators such as the ones I mentioned in post 7 who spent five years scrounging around in bat caves with nothing to show for it.
These questions have now become matters of urgent political importance. Virologists have tools to find new viruses and they are going to keep finding them. Without firm criteria to establish causality, the public is helpless at the hands of the ‘experts’. There can no point in arguing on the basis of facts because the interpretation of those facts is what is at stake and essentially it comes down to who has the power to enforce their interpretation. With the corona event we have seen ICTV appoint a working group to officially announce a ‘new’ virus. Their decision is final. There’s no point in arguing with it because there are no criteria by which to argue against. Similarly, the WHO officially declared a new disease. They broke their own standards to do that but who can argue against them?
This is not the way that science as we traditionally understand it is supposed to work. It seems that analytical problems in both virology and microbiology are leading us in the direction of having to accept expert opinion. Why not just address those analytical problem? Could it be that the entire fields of virology and microbiology are on the wrong path? The underlying problem in both cases seems to stem from the requirement in western philosophy to assign ‘essential’ attributes to things. As this debate is right at the core of corona event, I will devote a future post to it and in particular to how the philosopher Wittgenstein could point the way forward out of this conundrum.
Conclusion: legibility and infection
A number of microbiologists and doctors have spoken out against the public health measures taken during the corona event including two doctors from California who explicitly discuss the modern ideas around ‘microbial health’ and how the lockdown and mask wearing are decidedly unhealthy given what we now know about the human microbiome and virome. Of course, none of them made it into mainstream discourse.
Against this backdrop of developments in microbiology, the political and public health response during the corona event seems absurdly simplistic. But it was following a pattern that I recognised from one of my favourite books: James C. Scott’s Seeing Like a State. It is no coincidence that our public health response has been about a hundred years out of date because the type of response we launched is straight out of the late 19th and early 20th centuries. It is an example of what Scott calls high modernism: the attempt to re-work society according to scientific laws. These attempts were run out of the public bureaucracy and involved re-structuring society for legibility so that bureaucrats could understand what was going on. It is all about top-down schemes and top down governance. Such schemes require a simplification of reality in order to work. Usually this involves re-structuring reality to be simple enough to do your scheme but it can also occur by simply ignoring anything that doesn’t fit your categories, like doctors and microbiologists who point out that your science is wrong.
The corona event ticks the box on all of Scott’s conception of such high-modernist schemes. There is the administrative re-ordering and simplification of society seen in lockdowns, compulsory masks, curfews and restricted movement. There is the overconfidence in science to address the problem, a confidence that can only occur by putting your faith in a version of germ theory that’s a hundred years out of date. There is the use of authoritarian state power seen in the police and the army. And there is a prostrate civil society that cannot resist state power seen in possibly its ultimate form of people literally being confined to their homes.
I encourage the reader to check out Scott’s book although I warn that a terrifying glimpse will open up about what possibly lies ahead of us. Such high modernist schemes brought misery and destruction on a grand scale but those schemes were mostly at the national level and mostly occurred outside of the West. The West now appears set to embark on a similar Quixotic adventure which it will try to enforce at the global level. The results could be devastating.
The fact is, our public health response has been the opposite of what modern microbiology would advise. Things in nature need to flow and that goes also for germs and our exposure to them. The forced wearing of masks, the locking of people in their homes, the shutting down of civil society stops that flow at the microbial level. It removes us from nature. Apart from the obvious damage it does economically, psychologically and socially, it also doesn’t work for our health. The mainstream debate and the entire focus of the public health bureaucracy has been on ‘infections’ and ensuring there is maximal legibility around this so that bureaucrats can stamp out said infections. We know from modern microbiology that such infections are a normal part of everyday life and so the public health response has essentially become a war on that everyday life.
As with so many of the things around the corona event, this should have been a non-starter. It seems so self-evidently wrong that we marvel that it even got done. But perhaps there is something else going on and perhaps that something else is actually part of the recent developments in microbiology.
Maybe the reason we cling to the germ theory of disease is because it preserves a deeper web of meaning around ourselves as individuals. The vista that microbiology is opening up for us is one where our own body is radically unseparated from ‘nature’. This challenges all kinds of notions around selfhood and touches on deep issues in morality. What is at stake here is the question of whether we have any control at all and what sort of control we have. Microbiology is giving us a glimpse into how little we control and we don’t like it one bit. Maybe the massive over-reaction has been an attempt to regain the appearance of control at all costs. In this the politicians and public health bureaucracy have, in my opinion, only been doing what the public wanted. The public health response was a cover for deeper philosophical and psychological problems.
In the final post in this series I will return to this theme of the philosophical issues that underlie the corona event. In the next post I want to talk about the concept of heroism. As the corona event unfolded the public cried out for ‘heroes’. This cry was in direct response to the existential crisis that corona afforded, not the public health requirements. The concept of heroism and heroic effort has come out in some very strange ways during the corona event. We’ll unpack them next.
All posts in this series:-