|Where da atoms at?|
Today's post adds atomic data to the tables of the previous post in this series (Quantum Biology - 6).
As in that previous post, the tables are in appendices with the only difference in the new appendices is that a column "AA (formula)" has been added (Appendix QB.7.1, Appendix QB.7.2, Appendix QB.7.3, Appendix QB.7.4, Appendix QB.7.5, Appendix QB.7.6, Appendix QB.7.7, Appendix QB.7.8).
That additional column is the molecular formula for the relevant amino acid (which was not provided in the previous tables).
II. Why Add That Column?
The numbers of atoms in codons did not match each other even though the amino acid they were said to "code for" was the same.
Adding the amino acid formulas does not solve the problem with the nomenclature used by aberrant microbiologists.
I added it to further enforce my argument that the dolls they are playing with do not tell a verifiable story.
III. It Boils Down To Atoms (Not Codons)
The only valid discussion however is what happens at the atom level, just below the molecule level:
"A complex mechanism is involved by which information flows from DNA to RNA and become enzymes and other proteins. The image was still rather schematic, though. The way a molecule functions cannot be known unless the structure of the molecule is first known.
"The ribosome is one of the most complicated protein/RNA complexes. It consists of hundreds of thousands of atoms. She [Ada Yonath] wanted to establish the exact location of each and every one of these atoms in the ribosome. Many scientists thought this was very difficult task. And it was indeed one.
"A property of the ribosome, that has fascinated scientists for a long time, is that it seldom makes any errors when it translates DNA/RNA-language into protein language.
If an amino acid is incorrectly incorporated, the protein can entirely lose its function, or perhaps even worse, begin to function differently. For the correct amino acid to be selected depends primarily on the base pairs formed between tRNA and mRNA.
However, this pairing process is not sufficient to explain the ribosome’s precision. Dr. Ramakrishnan’s crystal structures of the ribosome’s small subunit have been crucial for the understanding of how the ribosome achieves its precision. He identified something that could be described as a molecular ruler.
Nucleotides in the small sub-unit’s rRNA measure the distance between the codon in mRNA and the anticodon in tRNA. If the distance is incorrect, the tRNA molecule falls off the ribosome. Using the ruler twice, the ribosome double-checks that everything is correct. This ensures that errors only occur about once per 1,00,000 amino acids."
(Mapping the ribosome at the atomic level, emphasis added). Thus, the exact number of atoms in codons, amino acids, and ribosomes is where "the rubber meets the road."
"Arguably, the ribosome is the most extraordinary of all the molecular
machines that mediate the processes of living systems. This will become
self- evident as we proceed" (The Ribosome Is a Molecular Machine, emphasis added).
IV. It Boils Down To The Atoms of Machines
Dredd Blog has, for years, pointed out the "greatest-ignored-issue", which is that the physical universe is mostly machine in nature: (The Uncertain Gene, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11; Putting A Face On Machine Mutation, 2, 3, 4; The Machine Religion, 2, 3; The New Paradigm: The Physical Universe Is Mostly Machine; Did Abiotic Intelligence Precede Biotic Intelligence?; If Cosmology Is "Off," How Can Biology Be "On?"), et cetera.
V. Closing Comments
The "playing with dolls" biology crowd needs to explain how the atoms got together because "they realized that they needed" a robosome to replicate stuff (On the Origin of the Genes of Viruses, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17).
I hope that breaks it down.
Oh, yeah, and now a word from the
polymerase real goo goo dolls.