PCR testing (from its inventor)

You may, like me, have heard rumours on the web that the inventor of the PCR test, Kary Mullis (he got a Nobel Prize for it) never intended his discovery to be used for diagnostics. Nobody can ask him about the current casedemic now, since he died last year. But a recent video , perhaps rather conspiratorialist in tone, nevertheless usefully collates some interesting footage of the man himself demonstrating why the current use of PCR is an abuse, pure and simple.

The first thing to note is that Mullis made himself unpopular in some circles by being scientifically rigorous. I was totally unaware that it was from him that the “conspiracy theory” that AIDS is not caused by HIV originated, and (as the video shows), he was on pretty solid scientific ground in saying so.

Asked to write a review paper on AIDS, his first sentence was “HIV is the likely cause of AIDS,” for which assertion he realised a reference would be desirable. Not only did he fail to find one in the literature on any search, but none of the HIV specialists he spoke to at conferences could give him one either. Eventually when he asked the discoverer of the link, Luc Montagnier, who also got a Nobel Prize, even he had no scientific backing to offer for the claim, eventually walking away from the conversation, as only Nobel winners are able.

Maybe that tells us something unwelcome about not only the Nobel Prize, but the state of science. The episode reminds me of the way that another scientist was unable to find any basis in the literature for the universally applied principle of the no-threshold linear dosage response. Scientists never take anything on authority, except (it seems) the most fundamental foundations of their work.

Mullis’s explanation of his test shows everything that is wrong with the management of COVID-19 by the myopic focus on “positive tests” (which have been re-named “cases” contrary to established medical norms). He explains the PCR process as a magnifier, pure and simple. But it is one of such huge sensitivity that, in Mullis’s opinion, if not applied carefully it will find virtually any molecule in any individual.

For this reason, it is only of use in disease management (a) when on other grounds the molecule is known to be causative and (b) when the number of cycles is limited to that known (also on other grounds) to produce positives only when sufficient significant molecules are present.

So if you know, based on the long-established standard I was taught at medical school, Koch’s postulates, that an organism causes a disease if a certain titre is present, then you can set the number of PCR cycles to detect above that level, and have a reasonable confirmatory test, subject to false positives and negatives (rates to be established by independent research, unfortunately not yet done for COVID-19 PCR). It was the lack of this correlation that led Mullis to doubt the role of HIV in AIDS.

As Wikipedia says, Koch’s work has had to be updated for the 21st century, especially because of viral infections, and it gives the following rather more complex list of criteria:

  • A nucleic acid sequence belonging to a putative pathogen should be present in most cases of an infectious disease. Microbial nucleic acids should be found preferentially in those organs or gross anatomic sites known to be diseased, and not in those organs that lack pathology.
  • Fewer, or no, copies of pathogen-associated nucleic acid sequences should occur in hosts or tissues without disease.
  • With resolution of disease, the copy number of pathogen-associated nucleic acid sequences should decrease or become undetectable. With clinical relapse, the opposite should occur.
  • When sequence detection predates disease, or sequence copy number correlates with severity of disease or pathology, the sequence-disease association is more likely to be a causal relationship.
  • The nature of the microorganism inferred from the available sequence should be consistent with the known biological characteristics of that group of organisms.
  • Tissue-sequence correlates should be sought at the cellular level: efforts should be made to demonstrate specific in situ hybridization of microbial sequence to areas of tissue pathology and to visible microorganisms or to areas where microorganisms are presumed to be located.
  • These sequence-based forms of evidence for microbial causation should be reproducible.

Essentially, none of these criteria have been met for COVID-19 PCR testing. At the general level, the later criteria correlating PCR with a demonstrated role for the particular virus in a particular disease of a particular organ has not been done. In other words, it is not yet proven that a specific Coronavirus is the cause of the specific outbreak we are seeing.

But at the “coal face,” for the most part PCR is not being used as a confirmatory diagnostic test in a disease. It couldn’t be, because there is no independent assay available to show that it is one disease caused by one virus, other than the PCR test itself – a circular argument.

Mainly, though, PCR is being used to diagnose people with ill-defined symptoms also present in many other viral conditions, and (in 80% of tests in Britain) as a screening test for people without symptoms, which as far as the Koch v2.0 postulates go, means “without disease.” Postulate #2: “Fewer, or no, copies of pathogen-associated nucleic acid sequences should occur in hosts or tissues without disease.”

But it gets worse, because the criteria HMG hands out to laboratories tendering to provide PCR testing contains no criterion for the number of amplification cycles. And as I said, Mullis believed that everybody contains pretty much any molecule, if you look hard enough. This is borne out by the fact that after 60 cycles, every test for COVID-19 is positive. So no lab would get away with running 60 cycles routinely.

But without the gold-standard test demanded by the postulates, any number set by a provider for the number of cycles is entirely arbitrary. It would be, perhaps, a little less arbitrary if the test were calibrated using patients clinically almost certain to have the SARS syndrome, but that has not been done – or if it has, it has not been translated into criteria for the quarter of a million tests being done daily at £200 a time (and you may multiply that up for the tests being done worldwide, because the scientific situation is the same).

When I kept Koi, I had a couple of new fish die the week after they were bought. When I complained that they must have some infection, the dealer asked me to bring a sample of the pond water to test. I knew it was fine, because I tested it myself regularly. But the guy in the shop, using the same test, left the test strip for far longer than the protocol before he read it – or rather, he kept reading it until, eventually, it turned positive for toxic nitrite. In that case, I knew he was wrong because he had gone beyond the manufacturer’s protocol. But in PCR testing, no equivalent protocol has been established. But whereas the issue for me was thirty quids’ worth of carp, the shoddy COVID practice is destroying many thousands of lives. To me, that matters.

My nitrite test might well be as useful in detecting COVID infections. And it would be a lot cheaper.

Because it belongs here, I will just repeat from a previous post that, uniquely in this epidemic, the WHO and the various national authorities have unaccountably discontinued the criteria for limiting tests to diseased patients, and requiring confirmation either by another kind of test (none exist) or at least by a test from a different lab (never going to happen). The H1N1 Casedemic of 2009 demonstrated how essential those controls were, which is why they have applied to every infection scare from then till now. It’s as if these authorities, knowing that public memory is short, deliberately conspired to produce another casedemic.

The alternative is that all the scientists at the WHO (maybe) entirely forgot all about how things went ten years ago, and that the CDC and so on, although often with the same senior staff, also forgot and simply rubber-stamped the WHO blunder. Your judgement call – chance is, after all, formally indistinguishable from choice. In this case, neither is very complimentary towards those in control of us.

For this reason, Kary Mullis, were he alive today, would not simply be annoyed that his test was being relied on too much to give accurate results – he would be saying that, as it is being used, it’s no better than necromancy. But you will be well aware that it is being used by governments to determine the fate of the whole of society, which means in practice its controlled demolition.

If it were discovered that the governments were consulting the spirit of Rasputin to make policy, they would lose more than their jobs: given the disastrous economic and medical outcomes, they would probably find themselves before an international human rights court. That won’t happen here, because the delusion is shared by most of the world’s governments, waving the banner of “Science.” But that doesn’t stop it being an entirely valid analogy to the inexplicable (because easily researched) abuse of Kart Mullis’s excellent discovery, for which he richly deserved his Nobel Prize.

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About Jon Garvey

Training in medicine (which was my career), social psychology and theology. Interests in most things, but especially the science-faith interface. The rest of my time, though, is spent writing, playing and recording music.
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