Another response to a virus supporter
Is there logic in how molecular biology finds a viral genome?
A virus supporter wrote:
The beauty of modern molecular biology is that we do not need to "purify" (always a relative term) a virus in order to identify it and study it. So no surprise that many agencies have not isolated/purified it.
As usual, I have more questions.
How does molecular biology identify a novel virus if it is not isolated/purified? Is metagenomic sequencing leading us to finding viruses? Is constructing genomes from fragments of genetic material real science? If it is, please answer these questions.
Let’s hypothesize there is a new virus in the patient sample. Suppose we have four thousand pieces of genetic material. It would likely be many magnitudes larger than that, but let’s go with it just for example.
There are a limited number of ways those can be put together due to the rules that must be followed in terms of matching base pairs on the ends of sequences, but it is still a large number.
How do we know which pieces belong to which intact entity (hypothesized virus or exosome or clathrin-coated vesicle or multivesicular body or endothelial tubuloreticular inclusion or some other structure) and how many entities those four thousand pieces came from? How do we know which pieces are formerly from intact entities and which pieces are non coding RNA?
If it is not feasible with even four thousand pieces, how can it be feasible with millions of pieces of unknown origin?
If we suspect it is a novel virus, i.e. not identified before, how can it be feasible to determine anything from a large number of pieces, many of which are similar to other hypothesized viruses which have been assembled in the same way?
Suppose we identify Strand X and it is contained in the supposed genome of Influenza A. How do we know if the strand from the patient sample that matches Strand X is from what is claimed to be Influenza A or is part of the novel virus we hypothesize is in the patient sample? Should we keep it in the genome we are constructing, or discard it?
How do we know if the genetic fragments in our sample came from human cells/proteins, viruses, bacteria, yeast, fetal bovine serum or monkey kidney cells?
If I gave you a box of Lego and asked you to construct a virc, you would ask me what a virc is -
Virc is a word I just made up. Shouldn’t science work the other way around? First we find something, then we find out what it is made of and it's properties and name it, not assume that things exist because we can make things from pieces we have available.
I have hypothesized it looks like a castle, but how would you know if you got it right if no one including me has ever seen a virc?
Legos only go together in certain ways, but there is a large number of ways they can go together.
Once a genome is determined, how do we know we have identified it correctly if we don't have an intact particle to compare it to?
The gold standard is an intact particle. No one has it for HIV, no one has it for SARS-CoV and no one has it for SARS-CoV-2.
Enzymes are smaller than viruses. HIV is said to contain an enzyme. Enzymes can be isolated, why can't viruses be isolated?
When I was about 5, I believed in a monster outside who made the windows rattle in the wind. Now I understand that there is wind, and there are windows that are loose and rattle, and there is the human tendency to try and coalesce a body of facts into something much more adverse sounding than the conditions actually create.
hiya what's a virc? I love the lego analogy and mini mouse, this is excellent
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