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| Fig. 1 What Could Go Wrong? |
I. Background
In a previous post the perplexing abundance of Toxoplasma Gondii ("Toxo") was discussed (How To Identify The Despotic Minority - 16, at section "IV. Deep Down").
Today let's take a look at Toxo genomes CM002035.1, CM002034.1, and CM002039.1, in terms of the codons and amino acids (links are in the appendices).
To set the stage I have constructed a Genetic Code table (APNDX Genetic Code) detailing the amino acids and codons in the official table, as well as a nucleotide/base pair table of the molecules the codons are composed of; a table of codons and amino acids in the Toxo genome (APNDX Amino Acids, Codons, Atoms); and a sorted list of them (APNDX Sorted Amino Acids, Codons, Atoms).
II. Format of Appendices
The appendices contain HTML tables composed of the details of portions of the Genetic Code and the genomes of Toxo in order of appearance in that genome (Amino Acids, Codons, Atoms) as well as sorted alphabetically by amino acid names (Sorted Amino Acids, Codons, Atoms) which lists amino acids, codons, and atomic formulas.
III. Purpose of Appendices
These appendices show that there is additional ambiguity in the atomic structures used by microbiologists to explain translation and transcription of DNA and RNA (which is more complex than historically thought to be, and more prone to misinterpretation too: Scientists discover double meaning in genetic code, Exonic enhancers: proceed with caution in exome and genome sequencing studies).
The Genetic Code appendix contains portions of the classical code used by scientists for many decades.
It shows the atomic differences between DNA codons and RNA codons associated with a particular amino acid (number and type of atoms in the codons variy even though the codon is said to "code for" only one particular amino acid).
The Sorted Amino Acids, Codons, Atoms appendix displays all the amino acids as a group so as to show how the atom counts of the various DNA and/or RNA codons is not the same in terms of "coding for" that particular amino acid (this means that the Toxo's ribosome must count the atoms before it can process the codon properly).
The Amino Acids, Codons, Atoms appendix lists the codons (and the amino acid they code for) in the order which they sequentially appear in the Toxo genome (only one, no repeats).
IV. Analysis
It would seem that the small brain considered (the ribosome) is quite artificially intelligent, even though it too (like the amino acids and codons) is just a group of atoms:
"Using a computer to simulate the interaction of 2.6 million atoms, Los Alamos National Laboratory researchers have re-created a tiny slice of one of the most fundamental genetic processes of life.
The lab simulated how a cellular machine called a ribosome follows genetic instructions to construct a complex molecule called a protein out of building blocks called amino acids. With 768 processors of LANL's 8,192-processor ASCI Q [human made] machine running for about 260 days, the researchers created a movie of the process. Previous views had shown only static snapshots."
(Lab computer simulates ribosome in motion, emphasis added). It took a human made super computer 260 days to depict what a microscopic machine does more quickly:
"the ribosome behavior that they simulated takes only 2 nanoseconds, or 2 billionths of a second"
(ibid). That somehow explains the time doll ("When the universe [doll] was very young — something like a hundredth of a billionth of a trillionth of a trillionth of a second (whew!) [the time doll was ... conjured ... shortly after that] — it underwent an incredible growth spurt", Quantum Biology - 9).
Go figure.
V. Closing Comments
Remember that there are multiple ribosomes in each Toxo cell and that there are multiple millions of Toxo cells in an infected carrier.
Those ribosome atoms make-up a ribosome machine that must 'artificially know' a carbon atom from a hydrogen atom, a hydrogen atom from a nitrogen atom, a nitrogen atom from an oxygen atom, and so forth.
That is because they must 'artificially know' each of the codon and amino acid atoms too.
And do all that ad infinitum, each in a few nanoseconds.
One wonders, then, what could go wrong with the experiment mentioned in Fig. 1 (Scientists grow human brain cells in rats to study diseases) because it seems to equate fairly closely to (Beating a dead horse).
Toxo somehow seems to be everywhere.
The next post in this series is here, the previous post in this series is here.