The Pet Theory Economy

Substack is a wonderful advance in journalism but we are going to have to pay close attention to the economic incentives. People need traffic and novelty drives traffic. As a result Pet Theories get defended as if their families livelihoods depend on it.

This week I was accused of getting JJ Couey fired from CHD. No evidence was provided. I was vilified for this act without evidence. Charles Rixey had a chuckle as he thinks JJ may have played a roll in getting him cut from CHD but Charles wasn’t going to state that as fact.

I have very few communication chains from CHD but they are clear as day in terms of my willingness to bury the hatchet and work with JJ despite his videos weaving me into his Scoobie Doo double agent narrative. I’ve tried to remain collegial with him but left that aside as his videos continue to obsess over my ‘misguided’ activities in this space.

His most recent tweet does emphasize what is going on in the attention economy. Poking holes in someones pet theory is now an interference with their ability to make a living.

It is as shallow as those ‘inciting violence’ canards where you must believe other people have no agency and they are automatons directed by your vocal chords. In this world, you are never responsible for your own actions as someone else ‘incited’ you to do it! With that simple twist in logic, free speech is annihilated.

If you believe in speech inciting people, then you must accept that there are ‘dumb’ people and smart people and thus you believe in a caste system. This naturally leads to one calling for more government to protect ‘dumb’ people from being incited by the smart ones. And voila, another caste system emerges out of the unaccountable holy government policing of free speech… only now directed at two lower castes of the ‘smart’ and ‘dumb’.

This is all circular. If you believe people can be incited by vocal chords then you believe people have no agency in their actions which begs the question of who vibrated your vocal chords? Were you incited to speak inciting comments? I digress on this point only emphasize that when some people are fired they look to blame everyone but their own actions.

Since this topic brewed up a large storm in the community I wanted to collate a lot of the literature on this topic. If you have not read my previous stack on this topic, it’s best to start on the Quasi-Species Swarm stack.

Much of this continued debate rests on Nick Hudson from PANDA escalating his ‘Coueyisms’. He was on a tear judging people for still believing in the Lab Leak →Pandemic theory. By his estimates no Pandemic occurred and the virus is a ghost. Many of us agree that the pandemic was exaggerated but the virus still circulated and caused illness. JJ Couey has added fuel to this fire claiming synthetic viruses can’t spread across the world as they mutate too quickly and therefore Infectious clones or ICs (plasmids) must have been seeded synchronously around the world to create a PCR mirage. The only methods to achieve high fidelity synchronous detection of SARs-CoV-2 is via this distributed parallel IC release Pet Theory.

Are infectious clones needed? Do they offer a fidelity benefit? I’ve covered why this is false in the previous substack but will expand on this some more here.

First, some of the fireworks-

You are NOT a good person unless you subscribe to this Coueyism. And the physicians recommending/selling IVM and other pandemic prep material are not good people as they buttress the Pandemic Prep Narrative.

You can imagine this opinion didn’t land softly.

Tweet

I am guilty of teasing Nick with sarcasm here which is likely why he fired off the above tweet about the meaning of my life:)

Paper This paper is only a few cases but shows how sequencing can narrow down transmission chains.

So lets examine the replication fidelity of the virus versus the Couey confusion over the fidelity of Infectious Clones.

2 approaches will be covered : In-vitro and In-vivo synthesis of RNA from DNA

In Vitro (No Cells)

You take this naked plasmid that encodes your 30kb virus and you run an RNA polymerase on it like T7 Polymerase. This will make RNA transcripts but they will have artifacts that will be present unless purified. This has been challenging for Moderna and Pfizer with just 4.2kb transcripts. Its even harder for 30kb transcripts encoding the whole viral genome.

There will be T7 polymerase fidelity issues with this approach that are more frequent than the viral polymerase replication machinery. My last post on this documents many of the paper that measure these respective polymerase fidelities. T7 polymerase doesn’t have a proof reading mechanism like the RdRp/ExoN polymerase in SARs-CoV-2.

Moderna also documents many of these fidelity issues. Template switching is the main concern as this creates recombination. Yes, the virus has recombination due to ExoN but these recombinations are limited/filtered out by the viral packaging machinery.

I have a whole post on this topic as Moderna mutated T7 Polymerase in 2023 to limit this artifact.

So all of the dots you see on that gel are mutated C19 genomes after T7 Polymerase tried to synthesize the C19 genome… And they need a massive clean up on isle 7. This is likely the driver of #blotgate. It is not RNA degredation. It is failure to synthesize with fidelity that is causing the messy RIN scores.

In the natural process of cells being infected by the virus, the genome signals the cell to create certain viral capsid proteins that help package a single full length and intact viral genome into a viral capsid. This has the impact of purifying the messy RNA synthesis. If the genomes recombine to something that is too long or too short the packaging signals will be destroyed and viral packaging will suffer.

Viral packaging purifies the samples.

Paper

Biology is smart and our in vitro emulations of it are often stupid. You can see this in papers that look at full length C19 genomes in the supernatent of infected cells and the full length genomes they find inside the pelleted cells.

Virions float.

They don’t centrifuge to the same compartment as pelleted cells and if you survey the two fractions you find over 50% of the genomes in the supernatent being full length genomes while less than 1% of the C19 genomes in the pelleted cells are full length. So you have to be very careful making estimates of full length viral genomes in sequencing studies. They entirely depend on which part of the cell culture you sequence. This is because viral packaging works.

So let’s imaging you spray these plasmids or these dirty In Vitro synthesized RNAs on people.

Will they transfect?

You merely need to look at the volumes of fact checkers that have stumbled on this point. They are correct to note that naked nucleic acids do not get into cells very easily as DNases and RNases destroy them. They need a viral capsid or an LNP to enter a cells. This is where the fact chokers end their debate.

Can some naked plasmids get in?

Many point to this substack I wrote as proof that ICs do infect people.

What they are failing to see is that this case was likely the result of E.coli containing the IC and the E.coli was colonizing people. Aerosolzied E.coli? Perhaps but then the metagenomic sequencing performed throughout the pandemic would contain the E.coli origin of replication and about 3-4Kb of other sequence from the plasmid that is required for that IC to persist in E.coli.

We don’t see this in the many metagenomic studies listed below. Butler et al. was covered in my prior quasi-species swarm substack. This paper actually sequences metagenomes from ground zero patients in NYC.

Metagenomes: you must understand sequences all RNA/DNA in the sample. They are hypothesis fee so when you don’t see your Pet Theory supported by them you should either nullify your hypothesis or hide the data from the cult you are trying to farm. JJ has chosen the later as he’s now dependent on his Pet Theory economy. Nick, has sadly gone all in on this cult and seems to have too much vitriol for anyone who doesn’t see it his way. There seems to be no rescuing him from his new found cult but we welcome you back once you drop the elitism regarding what everyone else should be doing.

In Vivo methods (Human cells make the RNA for you)

Once plasmids are in the cell, they rely on the same machinery as the virus (RdRP/ExoN) to replicate. There is no reason to believe this RNA would have any different fidelity than the virus traveling through the human population. One must also realize that alot of coronavirus swarm isnt ploymerase fidelity issues but instead APOBEC driven mutations from the host attacking the virus. This is a topic covered on the Quasi-Specied swarm post.

Let’s look at the metagenomic Sequencing data

Where are the Couey plasmid backbones in the metagenomic sequencing of patients? They cant be found? Did JJ ever mention this fact to his community of adherents?

Occasionally plasmids are found at very low levels in some NCBI sequencing archives but most of these have been itemized to be Index hopping & Lab contamination (sequencing contamination) and none have had exact sequences as SARs-CoV-2. Good people to follow on this are Dr. Steve Massey and Dr. Steven Quay.

The figure in Butler et al. is worth re-emphasizing. The Red parts of this chart on the left show patients where the highest % of reads in the tissue are SARs-CoV-2!! So the virus mRNA is majority of the RNA in the tissue! It swamps all Human RNA and if you think that is a ghost, you are a biological moron.

They also look at which human genes are differentially expressed as a result of infection. Look at that! Olfactory receptors are down regulated which explains the loss of taste and smell.

They go on to perform spatial transcriptomics of patients who died from the virus.

This is very compelling evidence that the viral RNA is present in huge numbers, causes down expression of olfactory receptors and localized to ACE2 expressing cells that have SARs-CoV-2 RNA in the aveoli. It doesn’t get more slam dunk than this. SARs-CoV-2 infects and causes a change in patient biology that is associated with disease and sometimes in rare cases, death.

So was this always around and we just missed it?

I suspect it was circulating earlier than December 2020 just based on the positivity of the early surveys on serology and qPCR of older samples. There is EVALI data and many dispersed data points that lead me to believe December wasn’t the release/leak data and there may even be US labs involved (UNC/RML). But we have to be careful with these suspicions as qPCR can cross react with earlier clades and ELISAs may have similar off target false positives.

Let’s look at the metagenomic sequencing of samples prior to 2020 or SARs-CoV-2 positive samples for other explanations .

They do not find these IC Ghosts? No plasmid backbones?

Thats amazing. A whole internet hoax has evolved with ZERO data that supports it in NCBI. This cult relies on people who will never look at sequencing data. Its the NoSeq Scoobie Doo Cult. Nearly as adept as “birds aren’t real” folks fostered by a bunch of people who will never learn the physics of electricity.

Paper of interest

Tigger warning. This paper uses the term “Pandemic Preparedness”. This will condemn all authors to Nicks Naughty list. Not Good people.

Paper

This is another study that uses metagenomic sequencing for SARs-CoV-2 tested people. Note all the positive have ONLY SARs-CoV-2 genomes. The Symptomatic but PCR negative samples have other respiratory viruses.

Paper

Note the Data Availability section. This does not exist for the Scooby Doo hypothesis that so easily entranced the PANDA team. Just handwaving, slandercasts and Twitch videos. What does it say about a Pandemic focused organization that has can’t traverse the DNA sequencing evidence? Their whole religion rests upon governments feeding them accurate mortality data while they raise their fist against the government. They can’t generate any novel data themselves. Everything is a re-interpretation of second hand data with opinions so strong they might as well have pink haired pronouns.

Let’s look at the paper that kicked all this madness off? Many have tried to claim this data was PCR generated and can’t be real. The methods section clearly shows they performed metagenomic sequencing and assembled this with Megahit. I have downloaded this data and reassembled it myself.

Ben Martin (No training in this field) has done this as well and tried to claim the data was a fraud because 4 bases ( out ~30,000) at the ends of the genome were not exactly the same when he assembled it. I showed him his errors using these assembly tools. He made a very ‘JV’ mistake and didn’t trim the DNA barcodes off the reads. When this error was shown to Ben, he refused to admit to any error and doubled down!

The conversation spiraled into accusations of me abusing him. This behavior of failing to course correct when shown overt and obvious errors should lead anyone taking his genomics takes with extreme caution. Not PANDA though. They absorbed his gospel as one more piece of evidence that everything C19 related is a fraud.

I find this to be an intellectual lethargy position. Its easy to elevate yourself from all Covid crimes by calling it all a farce. By doing so , you don’t actually have to get into the weeds and sort which parts are fact from fiction.

Here we have another ‘No Novel Pathogen’ celebration despite the data from PANDA being embarrassingly slipshod.

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This relates back to this post.

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So you can see why PANDA has gone off the genomic rails. There is a ‘No virus’ software engineer who is just learning bioinformatics and trying to construct a narrative that no viruses exist because he doesn’t know how to the use the tools he just learned last week. I’ve admired Be’ s work in mortality data but his obstinance to admit error in areas where I am a subject matter expert, means I can never trust any of his work again.

The field of handling high throughput sequence data is vast. It takes years to master these tools. There are PhD programs dedicated to simply handling these data correctly in light of the biological question at hand. You don’t learn all of these pitfalls running the programs for the first time. You learn them from being burned and wrong 100 other times.

You have to be able to course correct from your errors and if you get stuck on this concept of ego vs error correction on your 1st DNA assembly, you’ll never amount to the legends in the field that have assembled 1000s and admit error all the time.

The other way you learn these tools fast, is you build your own light-saber and are forced to fight with it in the market place to capture 30% market share. Our team did this with SOLiD sequencing and competed vigorously with Illumina for half a decade. Many of these bioinformatics tools had to be rewritten to handle the data torrents these sequencers produced (they were 1000- 100,000X the data torrent of previous sequencers). If you didn’t get over artifacts like this, you lost market share very quickly.

When someone in PANDA (I departed from their organization this week) highlights these problems, they are accused of picking on people. The 30 years of experience I have working on the human genome project, inventing novel DNA sequencers that enable Ben to even play with this data are all irrelevant. It’s about emotions, tweet etiquette, and hypothesis hunting…. Or my life has no meaning without praying to Coueyisms:)

Let’s get back to Metagenomics of SARs-CoV-2:

Have some metagenomic analysis found SARs-CoV-2 like sequences that pre-date the pandemic?

Not entirely.

These are often just PCR positive samples and without careful sequence analysis, they may be false positives.

Paper link here

This ‘No Pandemic’ Vitriol is a Distraction.

The mortality from the vaccines is hitting a younger age demographic. When adjusted for Quality Adjusted Life Years (QALY), the vaccine has likely wrecked more lives than the virus and the vaccine is something you can entirely avoid. You might be able to argue that pandemics only matter if they create death but people’s behavior is often simply guided by avoidance of pain or illness. Illness with SARs-CoV-2 has been thoroughly documented. You can hold this concern while fully protesting a centralized pandemic response. Voicing this concern or selling home treatment therapies does not ‘Incite’ pandemic preparedness. We are back to the crux of Nicks argument which is that people shouting treatment/vax concerns are ‘inciting’ Pandemic Prep concerns. This is a fallacy of agency. You can be 100% aligned with Nick on the risks of pandemic planning and still be concerned about Fauci using tax money to play with small pox in Boston. And physicians selling decentralized home remedies for any future virus are real physicians in my book. Teach everyone to take their health into their own hands and exit the Fiat Medicine system.

To close this out…

Lets have a look a ‘PANDA distraction’. A patient that is Vax antibody positive for 2 years. No nucleocapsid but clinical symptoms suggestive of spikeopathy.

Tweet link

PANDA would claim the virus doesn’t exist (‘to any reasonable definition’) and you won’t stop vaccines until you adopt our holy cloth and declare viruses can’t pandemic.

Others might claim it would have been so much worse with the virus.

OK.. Others would look at the patient in front of them ignore all this noise.

What gives you more spike mRNA?

For SARs-CoV-2 Peak viral load = 100B gRNAs. And most people do not hit peak viral load as they get and clear the virus asymptomatically.

There is no such partial dosing with the vaccine. Everyone gets the same dose and with gov mandates it hits ~70% of the people. The vaccine injects 43 Trillion modRNAs/100ug dose. Many repeat this 4 times.

In summary, the vast majority of acute harm once adjusted for QALY is from the needle. We can’t stop viral spread. We may be able to restrict funding for reckless GOF research, particularly if its goal is to make a lethal vaccine for the mess they create.

People focusing on all aspects of this crime are good people. You don’t need to join some myopic tribe that declares only one chapter of this hell-scape as being authentic. Any such tribe should be doubly questioned if the myopia is feeding some Pet Theory economy. It is this very non-tolerance to alternative ideas that enabled Fauci fascism to reign supreme with ScienceTM.

I know this was long but hope this was helpful.