On site reproduction with new hands and witnesses
This week Simon Goddek, PhD (@drgoddek.com) and Randall Bock, MD (@DrRandallBock) paid us a visit at Medicinal Genomics in Beverly Mass.
Nepetalactone Newsletter is a reader-supported publication. To receive new posts and support my work, consider becoming a free or paid subscriber.
We wasted no time putting them to work qPCRing Pfizer vaccines
Simon ran 16 replicates next to 8 run by myself. For someone who doesn’t pipette on a daily basis, Simon has excellent qPCR hands. His samples are in aqua (Spike) and red (Ori). Right on top of each other. This is 2µl of the vaccine so just 1/150th of the dose delivering CTs in the 15-16 range.
My samples are in blue(spike) and Green (Ori). The samples with the odd slope were in A4 at the top of the plate and likely didn’t seal well. Likely an Edge effect on the thermal cycler but the CTs are only slightly delayed.
The signals at 35-37 are NTCs. They are fractionally positive which means some are undetected and some are detected suggesting we may be at the single molecule threshold in our NTCs. The NTCs are more prone to Ori background. Dr. Lee pointed out this is likely the result of the residual plasmid used to make the polymerases in most qPCR kits. The spike is only positive in 1/3 NTCs. Notice the people who make polymerases can eliminate their plasmids from qPCR kits 1 million fold better than Pfizer can remove the plasmid from their vaccines.
Why? qPCR kits are a competitive market and if you make kits with too much shit in them, people go and buy clean kits. After all, people performing DNA amplification are going to be the first people to find your mistakes.
Pfizer on the other hand, enjoys mandates, liability waivers and makes it really hard for anyone to perform research on the material they insist needs to be injected into your children. So naturally, they have no incentive to clean this up.
We did make some tweaks compared to our published protocol. Since we were eager to get to dinner we hacked the qPCR protocol back to 30 sec extensions and removed the initial 50°C for 10 minute RT step. This being qPCR, the RT step is a superfluous.
Signal was evident in 25 minutes and this was a 59 minute cycling protocol in total.
Is this really an independent reproduction? Only partially.
In this case, we have different hands, running the qPCR in our lab with the same vials we have used before and getting shocking amounts of qPCR signal in the test. We have witnesses who can see the actual Pfizer vial being pipetted directly in to the qPCR mix and help inspect if we are playing any funny games. This lab visitation was something many people complained about regarding the regulation of the manufacturing of the vaccines. Most labs went unvisited and just ‘Trust Me Bro’ rubber stamps.
Stay tuned as we have heard of two other labs that are currently testing other vials with qPCR and finding the dsDNA.
This is a good time to reflect on John Ioannidis work.
50% of peer reviewed research doesn’t reproduce itself. We have already had multiple labs reproduce this work before it gets through Peer Review.
Reproduction trumps peer review every time.
Many view complaints against Peer review as a lazy cop out, but we don’t just bitch about the broken peer review system. We have pioneered blockchain based systems for Peer to Peer, peer review to help address this replication crisis in traditional peer review.
When people ask you “has it been peer reviewed?” stop and correct them.
The right question is “has it been reproduced?”.