The Unglossed Resource Hub
The Unglossed Resource Hub
More adventures in brute-force genomic analysis.
This page will serve as a repository for all my resource uploads, which will hereafter be linked in the footer of future posts. Eventually I hope to mirror this page on github or another more functional site.
As a metaphorical champagne-bottle to crack against the hull, I present my text-based map of the SARS-CoV-2 sequence. As with the spike amino acid map, it comes with a user-assumes-risk warning (translation: Use other sources or your own work to verify specific data in the map, as I may have made who-knows-what errors in collating and calculating values).
Contents:
Regarding SARS-CoV-2 and the Spike Protein
The SARS-CoV-2 Sequence Map (↓)
SARS-CoV-2 Spike Protein Map (↗)
SARS-CoV-2 Spike (and other structural genes) sequence alignment (↗)
The problem with the standard “WIV-GOF” origin theory (↗)
Omicron Origins: Summary / Spoiler (↗)
Regarding Spike, N, modRNA, and prions (↗)
The case for excess deaths in 2021 being primarily a result of the virus:
Regarding Covid vaccines
How truncated RNA’s from good manufacturing practice gaps may cause “Russian Roulette” outcomes in mRNA vaccines (↗)
Examining the biological plausibility of “severe efficacy” — IgG and lower respiratory tract immunity (↗)
Post-vaccine “breakthrough” infections and IgG4 — trapped with tolerance forever? (↗)
The 60 Day RNA Mystery: Spoiler / Summary (↗)
Regarding other viruses, and biology stuff
The case for polio as a “needle-borne plague” that clearly begins with the use of diphtheria anti-toxin in 1894 (↗)
Explaining memory B Cell remodeling and “imprinting.” (↗)
Is RNA virus evolution actually “fast”?, a.k.a. the “should variants actually happen series”:
The history of classic influenza virus research (↗)
The case for the 1918 flu virus just being a regular flu virus (↗)
“CUGA” genetic code map and user guide (↗)
OAS-is-not-real stuff (↓)
Bird flu outbreaks timeline (↗)
Vaccine study biases and built-in illusions (not always pro-vax) (↓)
SARS-CoV-2 and the Spike Protein
11.22.2022: The SARS-CoV-2 Sequence Map
What novel insights are possible when analyzing the SARS-COV-2 sequence “in the raw,” rather than using algorithms and scripts to fish for signatures trained on other genomes? Can the human brain’s pattern-recognition machine help decipher the virus’s evolutionary landscape?
There was only one way to find out, though it obviously carries a high risk of error; and that was to copy-paste the whole 29.9k genome by hand. Further user-guidance and commentary is included in the shared file.
The bottom of the document contains an unmapped copy of the sequence, which is no less useful for facilitating insight, imo. Because the SARS-CoV-2 RNA molecule is a physical object, how it “looks” is part of the story of how it works. For example, did you realize how much of the SARS-CoV-2 genome, even though it codes for all sorts of amino acids, is written using uracil repeats of four or longer (represented conventionally as “t,” and I have replaced c with “w”)?
For this reason, the infamous Furin Cleavage Site insert really does stick out like a sore thumb. I can find it without text-search:
Predictably, this favoritism for u-repeats, and a lesser preference for a-repeats, leads to an unusual prevalence of normally not-biologically-common “F,” “N,” and “K” residues in the virus’s proteins. The other notes section presents the math in question.
SARS-CoV-2’s genes can be thought of as a form of molecular poetry; they must adhere to strict formatting rules, limiting what the virus is able to “say” and how it is able to say it, just as surely as a haiku.
Alternately, one may imagine SARS-CoV-2 as a html file that somehow has to embed the “mark-up” into the text that will show on the screen — as if the sentence you just read somehow also programmed its own font, borders, responses to zoom commands, etc. Again as the “other notes” section in the map discusses, this has strong implications for the evolutionary landscape of the virus in the wild.
Overall, this endeavor was unsurprisingly tedious, yet far more productive than I had expected. I feel that I have a robust theory for explaining stabilizing selection in coronaviruses, though it may not be novel (it isn’t mentioned in Edward C. Holmes’ text, however).
11.16.2022: The Spike Protein Map
3.23.2023 SARS-CoV-2 Spike (and other structural genes) sequence alignment
3.17.2023 The problem with the standard “WIV-GOF” origin theory
7.13.2022: Omicron Origins: Summary / Spoiler
See also: No strong case for all the VOCs being lab-made (yet).
10.3.2022: Regarding Spike, N, modRNA, and prions
The case for excess deaths in 2021 being primarily a result of the virus
Resources in support of my argument that “American excess mortality does not reflect Covid vaccine harms (yet)”:
"Covid cases" vs. middle aged excess deaths - 25 most populous US states (↗)
(Counter-biased) survey evidence for high unvaccinated deaths (due to resumed medical mistreatment) in the “Delta” wave (↗)
US cardiac / circulatory-system deaths, 2020 - 2022 (↗)
Covid vaccines
1.22.2023: How truncated RNA’s from good manufacturing practice gaps may cause “Russian Roulette” outcomes in mRNA vaccines
(Includes results from Fertig, et al. showing no expression of spike on Pfizer-transfected PMBC cells.)
3.9.23 Examining the biological plausibility of “severe efficacy” — IgG and lower respiratory tract immunity
1.19.2023 Post-vaccine “breakthrough” infections and IgG4 — trapped with tolerance forever?
3.14.2022: The 60 Day RNA Mystery: Spoiler / Summary
Other viruses, and biology stuff:
9.21.2022 The case for polio as a “needle-borne plague” that clearly begins with the use of diphtheria anti-toxin in 1894
Is RNA virus evolution actually “fast”?, a.k.a. the “should variants actually happen series”:
RNA viruses do not always mutate quickly; flu is not as dynamic as it seems (↗)
Coronaviruses are not actually proven to mutate to evade immunity; evidence for a prior coronavirus “pandemic” in 1889 is weak (↗)
SARS-CoV-2 did not mutate quickly in 2020 (↗)
7.20.2022: The history of classic influenza virus research
8.21.2022: The case for the 1918 flu virus just being a regular flu virus
8.30.2022: OAS Literature review (table)
https://unglossed.substack.com/i/70716725/oas-reviewed-the-table
9.13.2022: Birth year pooled antibodies for original “OAS” studies
https://unglossed.substack.com/i/73251297/resource-upload-birth-year-pooled-antibodies
2.17.2022 “CUGA” genetic code map and user guide
8.9.2022: Bird flu outbreaks timeline
5.8.2022: Understanding sliding window illusions, “not-on-deathbed”-bias, and the “immortal unvaccinated problem”
See also: The “immortal vaccinated problem.”
Essentials from elsewhere:
The SARS-CoV-2 protein portfolio:
https://zhanggroup.org/COVID-19/index.html#table1
Visualizing SARS-CoV-2 subgenomic RNA regulation:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8539008/
LNP structure:
https://www.sciencedirect.com/science/article/pii/S0378517321003914
Pfizer Nonclinical report, Australia
https://www.tga.gov.au/sites/default/files/foi-2389-06.pdf
Maria Gutschi on mRNA Covid vaccine quality control failures:
More to be added. The Spike Protein map also serves a hub of relevant links.
Front toward enemy (The zoonati files):
“The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2”
https://www.science.org/doi/10.1126/science.abp8337
“The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic.”
https://www.science.org/doi/10.1126/science.abp8715
Ty Barney
Brian ... you GOT to watch this one. I have no words, but I think among all people ... you are going to find it interesting.
https://www.twitch.tv/videos/1660073740 (start at 04.00)