You’ve probably come across the name Kary Mullis recently, via social media. He’s best remembered for his invention (along with a team of other researchers) of the Polymerase Chain Reaction, or PCR for short (and for many biology students was probably immortalised in their memories via this earworm of an advertisement¹).
This turned out to be a very powerful tool, often used in combination with genome sequencing, for medical researchers and other scientists. It’s been used for everything from determining paternity, forensic testing, ancient DNA (aDNA) work on human ancestors (and other species), obtaining enough DNA from a specific gene for research on genetic disorders, and more besides, including identifying the presence of SARS-Cov-2. If you’d like to learn more about the technique, there’s a good explanation here, and teachers might find this video by the Amoeba Sisters useful with their classes.
Mullis & his colleagues² patented the invention in 1985, and in 1993 he received the Nobel Prize for his work.
Now, I’ve mentioned the patent quite deliberately, because I’ve seen it claimed that Mullis said PCR could not be used to identify the presence of particular pathogens. So, here’s a link to the patent, which states – in the first sentence of the abstract – that the invention (PCR) is a process for amplifying and detecting any target nucleic acid sequence. This is expanded on page 14 of the document: the technique is for amplifying existing nucleic acid sequences if they are present in a test sample and detecting them if present using a probe. And then, on page 22:
The method herein may also be used to enable detection and/or characterisation of specific nucleic acid sequences associated with infections diseases.
And on the following page:
Various infectious diseases can be diagnosed by the presence in clinical samples of specific DNA sequences characteristic of the causative microorganism [including bacteria, viruses, and parasites] … Specific amplification of suspected sequences … could greatly improve the sensitivity and specificity of these [existing] procedures.
It’s absolutely clear from this document that Mullis and his fellow researchers/inventors intended the technology to be used to detect the presence of pathogens that cause infectious diseases.
So, where has the confusion come from?
Well, sadly, by 1995 Mullis had become something of a scientific contrarian: he argued that the Human Immunodeficiency Virus (HIV) was not the cause of AIDS, an idea he mentions in his autobiography (Dancing Naked in the Mind Fields). He also published an alternative hypothesis³ for the origin of the disease, and discussed his ideas in this interview. This claim, by Mullis and others, went on to have deadly consequences for AIDS patients in South Africa.
Now, given the use of PCR to identify the presence of HIV in AIDS patients, claiming that HIV was not implicated in AIDS must surely have involved a certain amount of mental gymnastics. However, as I’ve written elsewhere, the specific words sometimes attributed to him on this subject actually came from someone else.
Meanwhile, the use of PCR in detecting the presence of pathogens – and in all those other applications – continues apace.
¹ and its sequel. Yes, I know, this totally dates me.
² It’s Mullis we remember for this, but in fact the patent lists multiple researchers in addition to Mullis: H.A. Erlich, N. Arnheim, G.T. Horn, R.K. Saiki, & S.J. Scharf. Erlich & Arnheim led the team that demonstrated conclusively that the technique worked.
³ In the absence of any actual data it is hardly surprising that this proposal didn’t take off.
Kurt says:
The problem was not the PCR test itself, but how it was used.
They were using cycle thresholds of 35,40 even 45, when it is well known that anything over 30 is pretty much useless. Even Fauci says it is beyond what will produce an accurate test. https://thehighwire.com/false-positive-covid-tests-will-extend-unjustified-lockdowns-fauci-admits-miniscule-accuracy/
The other problem is using it exclusively (without other clinical evaluation) to determine a Covid-19 “case”. The test only shows the presence of SARS-CoV-2, but that does not mean you have the disease, COVID-19. That you are sick or infectious or spreading the virus.
So now that they are done whipping everyone into a false state of fear and the vaccine profiteers are raking in their billions, NOW the CDC says those CTs are too high and have reduced the cycle limit to 28! And guess what for? To test so called “break through” cases of the vaccinated! Isn’t that convenient, now that they want to make the vax look more effective than it is… Suddenly the CTs they used all last year are now too high!
https://www.anhinternational.org/news/global-opposition-to-vaccine-programme-grows/
Alison says:
The problem was not the PCR test itself, but how it was used.
This is not the claim I’ve examined in my post. However…
In your comment about Dr Fauci you’ve cited not an actual research paper but something by one Del Bigtree. Bigtree is a television producer, not a scientist or a medical researcher, & he’s well-known for cherrypicking information. Try again.
The test shows the presence of the virus. It’s well documented that people can have an symptomatic infection (that is, the virus is present but has not caused clinical disease) but can still spread the virus to others. This recent systematic review demonstrates that quite well: https://www.acpjournals.org/doi/full/10.7326/M20-6976
Annals of Natural Health – really? That is hardly convincing evidence, on multiple fronts. How about presenting some high-quality scientific research to support your viewpoint? Or perhaps learning more about how the tests operate. The PCR tests used include a report at the end of each replication cycle that makes it very obvious when a positive result for the virus is first detected. Low CT reports are active infection. Higher CT results could represent either early infection, or historical infection. Which is why, in NZ, we do repeat testing of everyone in managed isolation & quarantine, to confirm their stage of infection.
Don says:
Well said my friend… However we wont get terribly from the true medical misinformation specialists from Cindy’s ministry of truth to which no doubt Alison, Helen, Hendy, Wilkes and Baker are all getting handsomely rewarded for.
These so called vaccine specialists relish in whipping up mass hysteria and panic amongst poor Kiwis to roll up their sleeves to take experimental gene therapy.
Alison – the CDC has stated there are too many false positives for an accurate test and are subsequently pulling this method of identification. Using a PCR test can quite easily damage the blood brain barrier too. Far too dangerous.
https://www.cdc.gov/sars/guidance/f-lab/assays.html
https://www.cdc.gov/csels/dls/locs/2021/07-21-2021-lab-alert-Changes_CDC_RT-PCR_SARS-CoV-2_Testing_1.html
After December 31, 2021, CDC will withdraw the request to the U.S. Food and Drug Administration (FDA) for Emergency Use Authorization (EUA) of the CDC 2019-Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel, the assay first introduced in February 2020 for detection of SARS-CoV-2 only. CDC is providing this advance notice for clinical laboratories to have adequate time to select and implement one of the many FDA-authorized alternatives.
In preparation for this change, CDC recommends clinical laboratories and testing sites that have been using the CDC 2019-nCoV RT-PCR assay select and begin their transition to another FDA-authorized COVID-19 test. CDC encourages laboratories to consider adoption of a multiplexed method that can facilitate detection and differentiation of SARS-CoV-2 and influenza viruses.
Mr. Carey Mullis (a Nobel prize winner) has stated this clearly. His tests were only ever designed for scientific research not bio or mainstream diagnostics.
I do love however that you all panic when a respected Doctor (true warrior amongst us) puts everything on the line (Peter Canaday) much like ex head of Pfizer – D4r. Mike Yeadon to condemn the illicit use of these synthetic jabs.
You all scramble to tell more lies to cover the truth. Lie lie lie…
Alison says:
which no doubt Alison, Helen, Hendy, Wilkes and Baker are all getting handsomely rewarded for. – a yes, the shill gambit; frequently pulled out when you have no better argument. How is it that you think people cannot hold a contrary opinion without being paid for it?
I’m not sure that you actually read the material at your first link. It’s archived for “historical purposes”, which suggests it’s out-of-date. The fact it says “in the absence of SARS-Cov transmission worldwide” reinforces that, since clearly that is not the case; transmission is global. It also points out that the use of RT-PCR helps to mitigate the problem of false positives.
I don’t think you understand the information at your second link either. At the moment the PCR test it mentions will tell you whether or not someone is infected with SARS-Cov-2. If they are not, the test cannot tell what else might be causing their symptoms. The CDC/FDA are requiring labs to change to a test that contains primers for both SARS-Cov-2 & influenza virus, and which is capable of differentiating between the two.
And no, Mullis didn’t state that at all. You’d know this if you read the patent documents instead of believing some misinformation that you saw on social media. https://patentimages.storage.googleapis.com/ec/14/bf/0a414f77b2d203/US4683195.pdf
From those documents: the first sentence of the abstract states that the invention (PCR) is a process “for amplifying and detecting any target nucleic acid sequence.” This is expanded on page 14 of the document: the technique is for “amplifying existing nucleic acid sequences if they are present in a test sample and detecting them if present using a probe.” And then, on page 22: “The method herein may also be used to enable detection and/or characterisation of specific nucleic acid sequences associated with infections diseases.” And on the following page: “Various infectious diseases can be diagnosed by the presence in clinical samples of specific DNA sequences characteristic of the causative microorganism [including bacteria, viruses, and parasites] … Specific amplification of suspected sequences … could greatly improve the sensitivity and specificity of these [existing] procedures.”
It’s absolutely clear from this document that Mullis and his fellow researchers/inventors intended the technology to be used to detect the presence of pathogens that cause infectious diseases.
And Peter Canaday? The Canaday with all the demonstrably incorrect statements in that two-hour video of his? You need to find a better “hero”.
The vaccine is not “illicit”, nor is it gene therapy as it doesn’t alter your genome. I’m fairly sure you know this. No-one is forcing you to take it, but how about you give up on trying to generate misinformed refusal among others? Aren’t you all about being able to choose for yourself?
gribbler says:
The claim that the CDC ‘have reduced the cycle limit to 28’ is erroneous.
They set this limit just for sequencing, since there needs to be a sufficient number of virions in the sample in order to reduce errors in the process. It has no bearing on the calibrated cycle limit for RT-PCR tests.
Alex says:
Indeed, having a sample taken from a swab does not qualify as means of reliable diagnostics. He said over and over again that to diagnose HIV with a PCR test was flat out wrong. Why so? So you swab, you move the swab sample through the air and maybe on the way from your nose to the container you catch a drop with what you were looking for. Given the very fact that PCR is a copy machine for just duplicating per cycle whatever is in the sample, you now test positive not due to the swab origin but due to what you caught from there to the container. It is pointless. That is why he was adamant about it being unfit for diagnostic purposes. It doesn’t matter how many times YouTube removes videos with interviews with Mr. Mullis, common sense is totally sufficient. PCR testing was intended for research as said time and again. And, yes, using PCR you can diagnose anyone with anything. Medical science has succumbed to mere statistics. And by how medical “science” propagates its findings you can reasonably argue that black socks cause cancer since based on statistics making that case is going to give you an overwhelming confirmation in any such study regardless of the fact that there is no causal relationship. The difference between real science and medical science is that real science cures people, medical science makes people sicker on average and all it addresses are symptoms, no root causes. It’s a show run by self-indulgent uncritical and reactionary bozos with little to no original ideas any more and most of all unwilling to be self-critical. Sad.
Alison says:
You missed the bit in the actual patent document that refers to its potential as a diagnostic tool?
Regarding your other claims – that which is asserted without evidence can be ignored.
Richard Kennard says:
Hello Alison
Kary Mullis didn’t become an AIDS “denier” He became sceptical that the HIV virus was the sole causative agent of AIDS. He wrote a paper that he wanted to reference with appropriate scientific literature that proved the hypothesis that HIV causes AIDS, and he couldn’t find it! He even asked Luc Montagnier and he didn’t know either.
On the subject of PCR. The FDA released this document https://www.fda.gov/media/134922/download On page 40 it states “Since no quantified virus isolates of the 2019-nCoV were available for CDC use at the time the test was developed and this study conducted, assays designed for detection of the 2019-nCoV RNA were tested with characterized stocks of in vitro transcribed full length RNA (N gene; GenBank accession: MN908947.2) of known titer (RNA copies/µL) spiked into a diluent consisting of a suspension of human A549 cells and viral transport medium (VTM) to mimic clinical specimen”
Other interesting things this document says are,
• This test cannot rule out diseases caused by other bacterial or viral pathogens.
• Detection of viral RNA may not indicate the presence of infectious virus or that 2019-nCoV is the causative agent for clinical symptoms.
• The performance of this test has not been established for monitoring treatment of 2019-nCoV infection.
• Positive and negative predictive values are highly dependent on prevalence. False-negative test results are more likely when prevalence of disease is high. False-positive test results are more likely when prevalence is moderate to low.
• Inhibitors or other types of interference may produce a false-negative result. An interference study evaluating the effect of common cold medications was not performed.
Do you have any scientific literature that shows that a “quantified” virus isolate has been used to confirm the accuracy of the tests before they were put into use? If not, is it possible that the tests are picking up particles that were used in the “Mimic”?
Alison says:
He denied the HIV-AIDS link, Richard: https://www.nature.com/articles/nature.2012.9737
assays designed for detection of the 2019-nCoV RNA were tested with characterized stocks of in vitro transcribed full length RNA (N gene; GenBank accession: MN908947.2) of known titer (RNA copies/µL) spiked into a diluent consisting of a suspension of human A549 cells and viral transport medium (VTM) to mimic clinical specimen” – this means that they used RNA copies of a SARS-Cov-2 gene (the N gene). So in answer to this: If not, is it possible that the tests are picking up particles that were used in the “Mimic”? – the “Mimic” comprised a SARS-Cov-2 genetic sequence.
This test cannot rule out diseases caused by other bacterial or viral pathogens. – because this test is not looking for those things. It is specific to SARS-Cov-2, and if it gives a negative result for that pathogen, then other tests would have to be used to confirm or rule out others. This is not a smoking gun.
Detection of viral RNA may not indicate the presence of infectious virus or that 2019-nCoV is the causative agent for clinical symptoms. – which is why we do serial tests on multiple days.
The performance of this test has not been established for monitoring treatment of 2019-nCoV infection. – because it is a test to detect the virus’s presence.
Matt Wood says:
The PCR test at 30 cycles will give a negative result 100% of the time. However at 60 cycles it will give a positive result 100% of the time. Hence, you can manipulate the test if you desire by what cycle threshold you use.
NZ uses 40 cycles which will create a degree of false positives. Australia uses 45 which will create a greater degree of false positives.
Hospitalisations are the true measure of a countries situation
Alison says:
The PCR test at 30 cycles will give a negative result 100% of the time. However at 60 cycles it will give a positive result 100% of the time. – I’m assuming you have a citation that supports this claim, because I doubt it’s correct. PCR can only detect something if a nucleic acid sequence belonging to that something is present in the sample in the first place. If there is a high viral load in the sample then you’ll get a positive result much earlier than the 3oth cycle.
Hospitalisations are the true measure of a countries situation – yeah, that’s not looking too promising in eg the US & Australia right now, is it?
Grant Jacobs says:
Hospitalisations are a measure of serious cases. Tests (of various types) measure infections. Neither is “the true measure”, they just reflecting different things.
Knowing the case rates is very important. It gives you a way to estimate the number of cases in the population, the spread, and is the base data for case hospitalisation rates, case fatality rates, etc. that reflect how well people are treated (or not, as the case may be).
There is no set Ct value for all PCR tests. PCR is a general approach that you make different tests from. There are literally dozens of different PCR tests just for COVID-19 (and thousands of PCR tests for other things). Each are calibrated against the samples they use. Ct values from different tests will have different meanings. As a clearer example PCR testing direct from saliva will involve a new PCR test regime, with its own calibrated Ct values.
In practice PCR tests for COVID-19 have very, very low rates of miscalling (true or false).
Philipp Legrum says:
The problem is that people are not smart enough to understand what
“Various infectious diseases can be diagnosed by the presence in clinical samples of specific DNA sequences characteristic of the causative microorganism.”
means.
You can diagnose with PCR only if you can ensure that the detected sequences (primers) are characteristic, i.e. these sequences may only occur in the entities the primers are set out to react with. That is usually the entities the primers are inspired by.
Characteristicness can, for purely logical reasons, only be ensured within a set of known oligonucleotides (admissible PCR search space).
Since we do not know about the behavior of the primers within the realm of unknown oligonucleotides, we cannot make any statement about the validity of the positive side of PCR-tests with regard to the question “Is a certain oligonucleotide present in the PCR’s educts?”.
The correct way to interpret PCR results is:
Test negative: exclusion succeded
Test positive: exclusion failed for unknown reason
The test needs to be interpreted in the logical contraposition of “If oligonucleotide to be detected present, then test positive.”
The global scientific shipwrecking of 2020 is related to the Wason 4-card-test and an erroneous believe that the following statement holds true: “It is highly unlikely that keywords taken from some text document match in some other unknown document.” (In fact the likeliness of this matching is unknown — that does not mean it is small.)
PCR-sensitivity: 100%
PCR-specificity: undefined with respect to presence of a certain oligonucleotide
PCR has not been understood as of 2021.
Alison says:
PCR has not been understood as of 2021. – this would come as news to the tens (hundreds?) of thousands of molecular biologists who routinely use this technique & apply it to their research.