Friday, January 28, 2022

Some Of My Best Friends Are Germs - 2

Coming To A GenBank Near You

In the first post of this series I bemoaned the way that RNA genomes were sequenced.

My specific beef was that 'U' (uracil) was not used by current genome database building techniques, instead 'T' (thymine) was used as it is in DNA sequencing (Some Of My Best Friends Are Germs, at Section II).  

I am more at ease now, since new techniques have been developed to solve the problem (MasterOfPores: A Workflow for the Analysis of Oxford Nanopore Direct RNA Sequencing Datasets).

There are some significant problems in the science of RNA nucleotide analysis (e.g. "the cause for the prolonged and recurrent production of viral RNA remains unknown", It's In The GenBank - 2) which is a critical exercise in civilization's practices that seek to avoid pandemics.

It's a process
The following three links evince a recent back and forth between two research teams concerning what causes "chimeric" (mixed) genome readings and illustrates some of the weaknesses in current virology research (Reverse-transcribed SARS-CoV-2 RNA can integrate into the genome of cultured human cells and can be expressed in patient-derived tissues; No evidence of SARS-CoV-2 reverse transcription and integration as the origin of chimeric transcripts in patient tissues, Response to Parry et al.: Strong evidence for genomic integration of SARS-CoV-2 sequences and expression in patient tissues).

In closing, let me remind readers that Dredd Blog has posted about these issues for many a year.

Dredd Blog hypothesizes that "the mass-slaughter-of-animals-for-food industry" and Big Pharma's promiscuous destruction of microbes, by indiscriminate killing, is a or the major cause of chimeric DNA and RNA (On The Origin Of The Home Of COVID-19, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27).

In other words, the microbes killed by antibiotics and other toxic chemicals spill DNA and RNA into the entity from which samples are extracted.

That spilled/mixed/chimeric material ("parts is parts") is later extracted (by DNA/RNA researchers) from the meta-host (cattle, chickens, pigs) which that microbe host was within.

When it was in the process of being damaged and/or killed that microbe was in the process of replicating its own DNA as well as any RNA of any viruses within it.

The replication was being done by the machinery inside that microbe, but its replication mechanisms were being damaged and/or destroyed as that microbe was in the process of being damaged and/or killed (in other words the genomes of the microbe and any viruses were rendered defective).

The first video below shows the death of the microbe host of the virus, and the spilling of its innards and replication machinery into the liquid of the meta-host.

The second video depicts the machinery inside the microbe host (not the meta-host) of the virus or viruses.

The third video is a snarky depiction of a tiny-by-comparison virus entering a vastly larger microbe to "take over its machinery" (as the news media would say).

The previous post in this series is here.

A friendly virus reports back to us about what it is like to enter into a vastly larger single-celled host "to take control over its highly complex machines" (The New Paradigm: The Physical Universe Is Mostly Machine).