Quantum Biology - 3

DNA is not alive

I. Background

The GenBank, which stores microbial and viral DNA/RNA (It's In The GenBank, 2, 3), also stores human DNA (Homo sapiens mitochondrion, complete genome).

Today's appendix shows the extracted genes, tRNA, and mRNA set forth in that GenBank homo sapiens GBFF file (Today's Appendix).

The genes, tRNA, and mRNA are extracted from the "ORIGIN" section of the GBFF file based on the locations set forth in that file.

With one difference, which is that the Thymine ('T' or 't') in the DNA nucleotides is changed into Uracil ('U' or 'u') in the appendix's RNA sequences.

That is because RNA is composed of 'U' molecules rather than 'T' molecules (but both have 'A', 'C', and 'G' molecules) as I pointed out in the nucleotide sequences of SARS-CoV-2 RNA in Quantum Biology - 2.

II. Sexy

A prominent microbiology site asked: "Do you consider mitochondrial DNA to be part of a eukaryote's genome?", to which I replied:

Good question. (It might be useful to say DNA is not RNA, i.e ACTG bp is not ACUG bp ... but even the genome databases @ GenBank GBFF files do not make that distinction in their bp data of RNA viruses ...)

But I digress ... so ... "Mitochondrial DNA is the small circular chromosome found inside mitochondria. The mitochondria are organelles found in cells that are the sites of energy production. The mitochondria, and thus mitochondrial DNA, are passed from mother to offspring ... Mitochondrial DNA, unlike nuclear DNA, is inherited from the mother, while nuclear DNA is inherited from both parents." (NIH).

Answer: yes. It is a matter of history and herstory.

 (Talmudic Question #193, Small Things Considered). Beauty may be only skin deep, but sexy goes all the way to the mitochondria and nucleus ... except for a few less sexy realms such as Leiolepis Ngovantrii:

"You could call it the surprise du jour: A popular food on Vietnamese menus has turned out to be a lizard previously unknown to science, scientists say.

What's more, the newfound Leiolepis ngovantrii is no run-of-the-mill reptile — the all-female species reproduces via cloning, without the need for male lizards."

(National Geographic, emphasis in original, cf. PDF here). On with the show:

"A virgin birth is expected this Christmas, though this particular nativity scene will be set in a zoo instead of a stable.

That's because the virgin in question is Flora the Komodo dragon, a giant lizard at Chester Zoo in England that has laid fertile eggs despite never having had a mate.

DNA tests confirmed Flora was the sole parent, says Chester Zoo curator of lower vertebrates Kevin Buley."

(Virgin Birth Expected at Christmas—By Komodo Dragon). Strange.

Getting back to the sexy mitochondrial human DNA:

"The mitochondrial genome is built of 16,569 DNA base pairs, whereas the nuclear genome is made of 3.3 billion DNA base pairs ... The mitochondrial genome contains 37 genes that encode 13 proteins, 22 tRNAs, and 2 rRNAs." (Nature)

"In humans ... mitochondrial DNA is inherited only from the mother..." (Wikipedia)

That's not all, so:

"Nuclear DNA (nDNA), or nuclear deoxyribonucleic acid, is the DNA contained within each cell nucleus of a eukaryotic organism. It encodes for the majority of the genome in eukaryotes, with mitochondrial DNA and plastid DNA coding for the rest. It adheres to Mendelian inheritance, with information coming from two parents, one male and one female—rather than matrilineally (through the mother) as in mitochondrial DNA.

(Wikipedia, Nuclear DNA). This kind of sexy is all about biological history and biological herstory.

III. Forward

Since the mitochondrial DNA (and RNA?) is more likely to experience mutations, let's review the quantum physics involved, an aspect (non-biological quantum photon-tunneling) that is very often overlooked in both human and virus genetic research:

"Furthermore, we find a large tautomeric occupation probability of 1.73 × 10⁻⁴, suggesting that such proton transfer may well play a far more important role in DNA mutation than has hitherto been suggested. Our results could have far-reaching consequences for current models of genetic mutations."

...

"Using both the C-G location and the A-U location in an RNA virus analysis seems quite likely to cut that Cornell University calculation in half or less (1.73 × 10⁻²)."

(Quantum Biology - 2). It is worth considering since the quantity of RNA mutations raises these questions.

IV. Closing Comments

Again, it is way past time to stop wondering "Why are RNA virus mutation rates so damn high" so we can, instead, experience more movements from Newtonian mechanics to Quantum Mechanics in biology.

The next post in this series is here, previous post in this series is here.

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Appendix QB-3

This is an appendix to: Quantum Biology - 3

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Gene list:

gene 1:

gtttatgtagcttacctcctcaaagcaatacactgaaaatgtttagacgg
gctcacatcaccccataaac

gene 2:

aataggtttggtcctagcctttctattagctcttagtaagattacacatg
caagcatccccgttccagtgagttcaccctctaaatcaccacgatcaaaa
ggaacaagcatcaagcacgcagcaatgcagctcaaaacgcttagcctagc
cacacccccacgggaaacagcagtgattaacctttagcaataaacgaaag
tttaactaagctatactaaccccagggttggtcaatttcgtgccagccac
cgcggtcacacgattaacccaagtcaatagaagccggcgtaaagagtgtt
ttagatcaccccctccccaataaagctaaaactcacctgagttgtaaaaa
actccagttgacacaaaatagactacgaaagtggctttaacatatctgaa
cacacaatagctaagacccaaactgggattagataccccactatgcttag
ccctaaacctcaacagttaaatcaacaaaactgctcgccagaacactacg
agccacagcttaaaactcaaaggacctggcggtgcttcatatccctctag
aggagcctgttctgtaatcgataaaccccgatcaacctcaccacctcttg
ctcagcctatataccgccatcttcagcaaaccctgatgaaggctacaaag
taagcgcaagtacccacgtaaagacgttaggtcaaggtgtagcccatgag
gtggcaagaaatgggctacattttctaccccagaaaactacgatagccct
tatgaaacttaagggtcgaaggtggatttagcagtaaactaagagtagag
tgcttagttgaacagggccctgaagcgcgtacacaccgcccgtcaccctc
ctcaagtatacttcaaaggacatttaactaaaacccctacgcatttatat
agaggagacaagtcgtaacatggtaagtgtactggaaagtgcacttggac
gaa

gene 3:

cagagtgtagcttaacacaaagcacccaacttacacttaggagatttcaa
cttaacttgaccgctctg

gene 4:

gctaaacctagccccaaacccactccaccttactaccagacaaccttagc
caaaccatttacccaaataaagtataggcgatagaaattgaaacctggcg
caatagatatagtaccgcaagggaaagatgaaaaattataaccaagcata
atatagcaaggactaacccctataccttctgcataatgaattaactagaa
ataactttgcaaggagagccaaagctaagacccccgaaaccagacgagct
acctaagaacagctaaaagagcacacccgtctatgtagcaaaatagtggg
aagatttataggtagaggcgacaaacctaccgagcctggtgatagctggt
tgtccaagatagaatcttagttcaactttaaatttgcccacagaaccctc
taaatccccttgtaaatttaactgttagtccaaagaggaacagctctttg
gacactaggaaaaaaccttgtagagagagtaaaaaatttaacacccatag
taggcctaaaagcagccaccaattaagaaagcgttcaagctcaacaccca
ctacctaaaaaatcccaaacatataactgaactcctcacacccaattgga
ccaatctatcaccctatagaagaactaatgttagtataagtaacatgaaa
acattctcctccgcataagcctgcgtcagattaaaacactgaactgacaa
ttaacagcccaatatctacaatcaaccaacaagtcattattaccctcact
gtcaacccaacacaggcatgctcataaggaaaggttaaaaaaagtaaaag
gaactcggcaaatcttaccccgcctgtttaccaaaaacatcacctctagc
atcaccagtattagaggcaccgcctgcccagtgacacatgtttaacggcc
gcggtaccctaaccgtgcaaaggtagcataatcacttgttccttaaatag
ggacctgtatgaatggctccacgagggttcagctgtctcttacttttaac
cagtgaaattgacctgcccgtgaagaggcgggcataacacagcaagacga
gaagaccctatggagctttaatttattaatgcaaacagtacctaacaaac
ccacaggtcctaaactaccaaacctgcattaaaaatttcggttggggcga
cctcggagcagaacccaacctccgagcagtacatgctaagacttcaccag
tcaaagcgaactactatactcaattgatccaataacttgaccaacggaac
aagttaccctagggataacagcgcaatcctattctagagtccatatcaac
aatagggtttacgacctcgatgttggatcaggacatcccgatggtgcagc
cgctattaaaggttcgtttgttcaacgattaaagtcctacgtgatctgag
ttcagaccggagtaatccaggtcggtttctatctacnttcaaattcctcc
ctgtacgaaaggacaagagaaataaggcctacttcacaaagcgccttccc
ccgtaaatgatatcatctcaacttagtattatacccacacccacccaaga
acagggtt

gene 5:

gttaagatggcagagcccggtaatcgcataaaacttaaaactttacagtc
agaggttcaattcctcttcttaac

gene 6:

atacccatggccaacctcctactcctcattgtacccattctaatcgcaat
ggcattcctaatgcttaccgaacgaaaaattctaggctatatacaactac
gcaaaggccccaacgttgtaggcccctacgggctactacaacccttcgct
gacgccataaaactcttcaccaaagagcccctaaaacccgccacatctac
catcaccctctacatcaccgccccgaccttagctctcaccatcgctcttc
tactatgaacccccctccccatacccaaccccctggtcaacctcaaccta
ggcctcctatttattctagccacctctagcctagccgtttactcaatcct
ctgatcagggtgagcatcaaactcaaactacgccctgatcggcgcactgc
gagcagtagcccaaacaatctcatatgaagtcaccctagccatcattcta
ctatcaacattactaataagtggctcctttaacctctccacccttatcac
aacacaagaacacctctgattactcctgccatcatgacccttggccataa
tatgatttatctccacactagcagagaccaaccgaacccccttcgacctt
gccgaaggggagtccgaactagtctcaggcttcaacatcgaatacgccgc
aggccccttcgccctattcttcatagccgaatacacaaacattattataa
taaacaccctcaccactacaatcttcctaggaacaacatatgacgcactc
tcccctgaactctacacaacatattttgtcaccaagaccctacttctaac
ctccctgttcttatgaattcgaacagcatacccccgattccgctacgacc
aactcatacacctcctatgaaaaaacttcctaccactcaccctagcatta
cttatatgatatgtctccatacccattacaatctccagcattccccctca
aacct

gene 7:

agaaatatgtctgataaaagagttactttgatagagtaaataataggagc
ttaaacccccttatttct

gene 8:

ctaggactatgagaatcgaacccatccctgagaatccaaaattctccgtg
ccacctatcacaccccatcct

gene 9:

agtaaggtcagctaaataagctatcgggcccataccccgaaaatgttggt
tatacccttcccgtact

gene 10:

attaatcccctggcccaacccgtcatctactctaccatctttgcaggcac
actcatcacagcgctaagctcgcactgattttttacctgagtaggcctag
aaataaacatgctagcttttattccagttctaaccaaaaaaataaaccct
cgttccacagaagctgccatcaagtatttcctcacgcaagcaaccgcatc
cataatccttctaatagctatcctcttcaacaatatactctccggacaat
gaaccataaccaatactaccaatcaatactcatcattaataatcataata
gctatagcaataaaactaggaatagccccctttcacttctgagtcccaga
ggttacccaaggcacccctctgacatccggcctgcttcttctcacatgac
aaaaactagcccccatctcaatcatataccaaatctctccctcactaaac
gtaagccttctcctcactctctcaatcttatccatcatagcaggcagttg
aggtggattaaaccaaacccagctacgcaaaatcttagcatactcctcaa
ttacccacataggatgaataatagcagttctaccgtacaaccctaacata
accattcttaatttaactatttatattatcctaactactaccgcattcct
actactcaacttaaactccagcaccacgaccctactactatctcgcacct
gaaacaagctaacatgactaacacccttaattccatccaccctcctctcc
ctaggaggcctgcccccgctaaccggctttttgcccaaatgggccattat
cgaagaattcacaaaaaacaatagcctcatcatccccaccatcatagcca
ccatcaccctccttaacctctacttctacctacgcctaatctactccacc
tcaatcacactactccccatatctaacaacgtaaaaataaaatgacagtt
tgaacatacaaaacccaccccattcctccccacactcatcgcccttacca
cgctactcctacctatctccccttttatactaataatctta

gene 11:

agaaatttaggttaaatacagaccaagagccttcaaagccctcagtaagt
tgcaatacttaatttct

gene 12:

taaggactgcaaaaccccactctgcatcaactgaacgcaaatcagccact
ttaattaagctaagccct

gene 13:

ctagaccaatgggacttaaacccacaaacacttagttaacagctaagcac
cctaatcaactggcttcaatct

gene 14:

aagccccggcaggtttgaagctgcttcttcgaatttgcaattcaatatga
aaatcacctcggagc

gene 15:

tggtaaaaagaggcctaacccctgtctttagatttacagtccaatgcttc
actcagccattttac

gene 16:

atgttcgccgaccgttgactattctctacaaaccacaaagacattggaac
actatacctattattcggcgcatgagctggagtcctaggcacagctctaa
gcctccttattcgagccgagctgggccagccaggcaaccttctaggtaac
gaccacatctacaacgttatcgtcacagcccatgcatttgtaataatctt
cttcatagtaatacccatcataatcggaggctttggcaactgactagttc
ccctaataatcggtgcccccgatatggcgtttccccgcataaacaacata
agcttctgactcttacctccctctctcctactcctgctcgcatctgctat
agtggaggccggagcaggaacaggttgaacagtctaccctcccttagcag
ggaactactcccaccctggagcctccgtagacctaaccatcttctcctta
cacctagcaggtgtctcctctatcttaggggccatcaatttcatcacaac
aattatcaatataaaaccccctgccataacccaataccaaacgcccctct
tcgtctgatccgtcctaatcacagcagtcctacttctcctatctctccca
gtcctagctgctggcatcactatactactaacagaccgcaacctcaacac
caccttcttcgaccccgccggaggaggagaccccattctataccaacacc
tattctgatttttcggtcaccctgaagtttatattcttatcctaccaggc
ttcggaataatctcccatattgtaacttactactccggaaaaaaagaacc
atttggatacataggtatggtctgagctatgatatcaattggcttcctag
ggtttatcgtgtgagcacaccatatatttacagtaggaatagacgtagac
acacgagcatatttcacctccgctaccataatcatcgctatccccaccgg
cgtcaaagtatttagctgactcgccacactccacggaagcaatatgaaat
gatctgctgcagtgctctgagccctaggattcatctttcttttcaccgta
ggtggcctgactggcattgtattagcaaactcatcactagacatcgtact
acacgacacgtactacgttgtagcccacttccactatgtcctatcaatag
gagctgtatttgccatcataggaggcttcattcactgatttcccctattc
tcaggctacaccctagaccaaacctacgccaaaatccatttcactatcat
attcatcggcgtaaatctaactttcttcccacaacactttctcggcctat
ccggaatgccccgacgttactcggactaccccgatgcatacaccacatga
aacatcctatcatctgtaggctcattcatttctctaacagcagtaatatt
aataattttcatgatttgagaagccttcgcttcgaagcgaaaagtcctaa
tagtagaagaaccctccataaacctggagtgactatatggatgcccccca
ccctaccacacattcgaagaacccgtatacataaaatctag

gene 17:

caaaaaaggaaggaatcgaaccccccaaagctggtttcaagccaacccca
tggcctccatgacttttt

gene 18:

aaggtattagaaaaaccatttcataactttgtcaaagttaaattataggc
taaatcctatatatctt

gene 19:

atggcacatgcagcgcaagtaggtctacaagacgctacttcccctatcat
agaagagcttatcacctttcatgatcacgccctcataatcattttcctta
tctgcttcctagtcctgtatgcccttttcctaacactcacaacaaaacta
actaatactaacatctcagacgctcaggaaatagaaaccgtctgaactat
cctgcccgccatcatcctagtcctcatcgccctcccatccctacgcatcc
tttacataacagacgaggtcaacgatccctcccttaccatcaaatcaatt
ggccaccaatggtactgaacctacgagtacaccgactacggcggactaat
cttcaactcctacatacttcccccattattcctagaaccaggcgacctgc
gactccttgacgttgacaatcgagtagtactcccgattgaagcccccatt
cgtataataattacatcacaagacgtcttgcactcatgagctgtccccac
attaggcttaaaaacagatgcaattcccggacgtctaaaccaaaccactt
tcaccgctacacgaccgggggtatactacggtcaatgctctgaaatctgt
ggagcaaaccacagtttcatgcccatcgtcctagaattaattcccctaaa
aatctttgaaatagggcccgtatttaccctata

gene 20:

cactgtaaagctaacttagcattaaccttttaagttaaagattaagagaa
ccaacacctctttacagtg

gene 21:

atgccccaactaaatactaccgtatggcccaccataattacccccatact
ccttacactattcctcatcacccaactaaaaatattaaacacaaactacc
acctacctccctcaccaaagcccataaaaataaaaaattataacaaaccc
tgagaaccaaaatgaacgaaaatctgttcgcttcattcattgcccccaca
atccta

gene 22:

atgaacgaaaatctgttcgcttcattcattgcccccacaatcctaggcct
acccgccgcagtactgatcattctatttccccctctattgatccccacct
ccaaatatctcatcaacaaccgactaatcaccacccaacaatgactaatc
aaactaacctcaaaacaaatgataaccatacacaacactaaaggacgaac
ctgatctcttatactagtatccttaatcatttttattgccacaactaacc
tcctcggactcctgcctcactcatttacaccaaccacccaactatctata
aacctagccatggccatccccttatgagcgggcacagtgattataggctt
tcgctctaagattaaaaatgccctagcccacttcttaccacaaggcacac
ctacaccccttatccccatactagttattatcgaaaccatcagcctactc
attcaaccaatagccctggccgtacgcctaaccgctaacattactgcagg
ccacctactcatgcacctaattggaagcgccaccctagcaatatcaacca
ttaaccttccctctacacttatcatcttcacaattctaattctactgact
atcctagaaatcgctgtcgccttaatccaagcctacgttttcacacttct
agtaagcctctacctgcacgacaacacata

gene 23:

atgacccaccaatcacatgcctatcatatagtaaaacccagcccatgacc
cctaacaggggccctctcagccctcctaatgacctccggcctagccatgt
gatttcacttccactccataacgctcctcatactaggcctactaaccaac
acactaaccatataccaatgatggcgcgatgtaacacgagaaagcacata
ccaaggccaccacacaccacctgtccaaaaaggccttcgatacgggataa
tcctatttattacctcagaagtttttttcttcgcaggatttttctgagcc
ttttaccactccagcctagcccctaccccccaattaggagggcactggcc
cccaacaggcatcaccccgctaaatcccctagaagtcccactcctaaaca
catccgtattactcgcatcaggagtatcaatcacctgagctcaccatagt
ctaatagaaaacaaccgaaaccaaataattcaagcactgcttattacaat
tttactgggtctctattttaccctcctacaagcctcagagtacttcgagt
ctcccttcaccatttccgacggcatctacggctcaacattttttgtagcc
acaggcttccacggacttcacgtcattattggctcaactttcctcactat
ctgcttcatccgccaactaatatttcactttacatccaaacatcactttg
gcttcgaagccgccgcctgatactggcattttgtagatgtggtttgacta
tttctgtatgtctccatctattgatgagggtct

gene 24:

actcttttagtataaatagtaccgttaacttccaattaactagttttgac
aacattcaaaaaagagt

gene 25:

ataaacttcgccttaattttaataatcaacaccctcctagccttactact
aataattattacattttgactaccacaactcaacggctacatagaaaaat
ccaccccttacgagtgcggcttcgaccctatatcccccgcccgcgtccct
ttctccataaaattcttcttagtagctattaccttcttattatttgatct
agaaattgccctccttttacccctaccatgagccctacaaacaactaacc
tgccactaatagttatgtcatccctcttattaatcatcatcctagcccta
agtctggcctatgagtgactacaaaaaggattagactgaaccgaa

gene 26:

tggtatatagtttaaacaaaacgaatgatttcgactcattaaattatgat
aatcatatttacca

gene 27:

atgcccctcatttacataaatattatactagcatttaccatctcacttct
aggaatactagtatatcgctcacacctcatatcctccctactatgcctag
aaggaataatactatcgctgttcattatagctactctcataaccctcaac
acccactccctcttagccaatattgtgcctattgccatactagtctttgc
cgcctgcgaagcagcggtgggcctagccctactagtctcaatctccaaca
catatggcctagactacgtacataacctaaacctactccaatgcta

gene 28:

atgctaaaactaatcgtcccaacaattatattactaccactgacatgact
ttccaaaaaacacataatttgaatcaacacaaccacccacagcctaatta
ttagcatcatccctctactattttttaaccaaatcaacaacaacctattt
agctgttccccaaccttttcctccgaccccctaacaacccccctcctaat
actaactacctgactcctacccctcacaatcatggcaagccaacgccact
tatccagtgaaccactatcacgaaaaaaactctacctctctatactaatc
tccctacaaatctccttaattataacattcacagccacagaactaatcat
attttatatcttcttcgaaaccacacttatccccaccttggctatcatca
cccgatgaggcaaccagccagaacgcctgaacgcaggcacatacttccta
ttctacaccctagtaggctcccttcccctactcatcgcactaatttacac
tcacaacaccctaggctcactaaacattctactactcactctcactgccc
aagaactatcaaactcctgagccaacaacttaatatgactagcttacaca
atagcttttatagtaaagatacctctttacggactccacttatgactccc
taaagcccatgtcgaagcccccatcgctgggtcaatagtacttgccgcag
tactcttaaaactaggcggctatggtataatacgcctcacactcattctc
aaccccctgacaaaacacatagcctaccccttccttgtactatccctatg
aggcataattataacaagctccatctgcctacgacaaacagacctaaaat
cgctcattgcatactcttcaatcagccacatagccctcgtagtaacagcc
attctcatccaaaccccctgaagcttcaccggcgcagtcattctcataat
cgcccacgggcttacatcctcattactattctgcctagcaaactcaaact
acgaacgcactcacagtcgcatcataatcctctctcaaggacttcaaact
ctactcccactaatagctttttgatgacttctagcaagcctcgctaacct
cgccttaccccccactattaacctactgggagaactctctgtgctagtaa
ccacgttctcctgatcaaatatcactctcctacttacaggactcaacata
ctagtcacagccctatactccctctacatatttaccacaacacaatgggg
ctcactcacccaccacattaacaacataaaaccctcattcacacgagaaa
acaccctcatgttcatacacctatcccccattctcctcctatccctcaac
cccgacatcattaccgggttttcctct

gene 29:

gtaaatatagtttaaccaaaacatcagattgtgaatctgacaacagaggc
ttacgaccccttatttac

gene 30:

gagaaagctcacaagaactgctaactcatgcccccatgtctaacaacatg
gctttctc

gene 31:

acttttaaaggataacagctatccattggtcttaggccccaaaaattttg
gtgcaactccaaataaaagt

gene 32:

ataaccatgcacactactataaccaccctaaccctgacttccctaattcc
ccccatccttaccaccctcgttaaccctaacaaaaaaaactcataccccc
attatgtaaaatccattgtcgcatccacctttattatcagtctcttcccc
acaacaatattcatgtgcctagaccaagaagttattatctcgaactgaca
ctgagccacaacccaaacaacccagctctccctaagcttcaaactagact
acttctccataatattcatccctgtagcattgttcgttacatggtccatc
atagaattctcactgtgatatataaactcagacccaaacattaatcagtt
cttcaaatatctactcatcttcctaattaccatactaatcttagttaccg
ctaacaacctattccaactgttcatcggctgagagggcgtaggaattata
tccttcttgctcatcagttgatgatacgcccgagcagatgccaacacagc
agccattcaagcaatcctatacaaccgtatcggcgatatcggtttcatcc
tcgccttagcatgatttatcctacactccaactcatgagacccacaacaa
atagcccttctaaacgctaatccaagcctcaccccactactaggcctcct
cctagcagcagcaggcaaatcagcccaattaggtctccacccctgactcc
cctcagccatagaaggccccaccccagtctcagccctactccactcaagc
actatagttgtagcaggaatcttcttactcatccgcttccaccccctagc
agaaaatagcccactaatccaaactctaacactatgcttaggcgctatca
ccactctgttcgcagcagtctgcgcccttacacaaaatgacatcaaaaaa
atcgtagccttctccacttcaagtcaactaggactcataatagttacaat
cggcatcaaccaaccacacctagcattcctgcacatctgtacccacgcct
tcttcaaagccatactatttatgtgctccgggtccatcatccacaacctt
aacaatgaacaagatattcgaaaaataggaggactactcaaaaccatacc
tctcacttcaacctccctcaccattggcagcctagcattagcaggaatac
ctttcctcacaggtttctactccaaagaccacatcatcgaaaccgcaaac
atatcatacacaaacgcctgagccctatctattactctcatcgctacctc
cctgacaagcgcctatagcactcgaataattcttctcaccctaacaggtc
aacctcgcttccccacccttactaacattaacgaaaataaccccacccta
ctaaaccccattaaacgcctggcagccggaagcctattcgcaggatttct
cattactaacaacatttcccccgcatcccccttccaaacaacaatccccc
tctacctaaaactcacagccctcgctgtcactttcctaggacttctaaca
gccctagacctcaactacctaaccaacaaacttaaaataaaatccccact
atgcacattttatttctccaacatactcggattctaccctagcatcacac
accgcacaatcccctatctaggccttcttacgagccaaaacctgccccta
ctcctcctagacctaacctgactagaaaagctattacctaaaacaatttc
acagcaccaaatctccacctccatcatcacctcaacccaaaaaggcataa
ttaaactttacttcctctctttcttcttcccactcatcctaaccctactc
ctaatcacata

gene 33:

cctattcccccgagcaatctcaattacaatatatacaccaacaaacaatg
ttcaaccagtaactactactaatcaacgcccataatcatacaaagccccc
gcaccaataggatcctcccgaatcaaccctgacccctctccttcataaat
tattcagcttcctacactattaaagtttaccacaaccaccaccccatcat
actctttcacccacagcaccaatcctacctccatcgctaaccccactaaa
acactcaccaagacctcaacccctgacccccatgcctcaggatactcctc
aatagccatcgctgtagtatatccaaagacaaccatcattccccctaaat
aaattaaaaaaactattaaacccatataacctcccccaaaattcagaata
ataacacacccgaccacaccgctaacaatcaatactaaacccccataaat
aggagaaggcttagaagaaaaccccacaaaccccattactaaacccacac
tcaacagaaacaaagcatacatca

gene 34:

tattctcgcacggactacaaccacgaccaatgatatgaaaaaccatcgtt
gtatttcaactacaagaa

gene 35:

atgaccccaatacgcaaaactaaccccctaataaaattaattaaccactc
attcatcgacctccccaccccatccaacatctccgcatgatgaaacttcg
gctcactccttggcgcctgcctgatcctccaaatcaccacaggactattc
ctagccatgcactactcaccagacgcctcaaccgccttttcatcaatcgc
ccacatcactcgagacgtaaattatggctgaatcatccgctaccttcacg
ccaatggcgcctcaatattctttatctgcctcttcctacacatcgggcga
ggcctatattacggatcatttctctactcagaaacctgaaacatcggcat
tatcctcctgcttgcaactatagcaacagccttcataggctatgtcctcc
cgtgaggccaaatatcattctgaggggccacagtaattacaaacttacta
tccgccatcccatacattgggacagacctagttcaatgaatctgaggagg
ctactcagtagacagtcccaccctcacacgattctttacctttcacttca
tcttgcccttcattattgcagccctagcaacactccacctcctattcttg
cacgaaacgggatcaaacaaccccctaggaatcacctcccattccgataa
aatcaccttccacccttactacacaatcaaagacgccctcggcttacttc
tcttccttctctccttaatgacattaacactattctcaccagacctccta
ggcgacccagacaattataccctagccaaccccttaaacacccctcccca
catcaagcccgaatgatatttcctattcgcctacacaattctccgatccg
tccctaacaaactaggaggcgtccttgccctattactatccatcctcatc
ctagcaataatccccatcctccatatatccaaacaacaaagcataatatt
tcgcccactaagccaatcactttattgactcctagccgcagacctcctca
ttctaacctgaatcggaggacaaccagtaagctacccttttaccatcatt
ggacaagtagcatccgtactatacttcacaacaatcctaatcctaatacc
aactatctccctaattgaaaacaaaatactcaaatgggcc

gene 36:

gtccttgtagtataaactaatacaccagtcttgtaaaccggagatgaaaa
cctttttccaaggac

gene 37:

tcagagaaaaagtctttaactccaccattagcacccaaagctaagattct
aatttaaactattctct

mRNA list:

mRNA 1:

aauagguuugguccuagccuuucuauuagcucuuaguaagauuacacaug
caagcauccccguuccagugaguucacccucuaaaucaccacgaucaaaa
ggaacaagcaucaagcacgcagcaaugcagcucaaaacgcuuagccuagc
cacacccccacgggaaacagcagugauuaaccuuuagcaauaaacgaaag
uuuaacuaagcuauacuaaccccaggguuggucaauuucgugccagccac
cgcggucacacgauuaacccaagucaauagaagccggcguaaagaguguu
uuagaucacccccuccccaauaaagcuaaaacucaccugaguuguaaaaa
acuccaguugacacaaaauagacuacgaaaguggcuuuaacauaucugaa
cacacaauagcuaagacccaaacugggauuagauaccccacuaugcuuag
cccuaaaccucaacaguuaaaucaacaaaacugcucgccagaacacuacg
agccacagcuuaaaacucaaaggaccuggcggugcuucauaucccucuag
aggagccuguucuguaaucgauaaaccccgaucaaccucaccaccucuug
cucagccuauauaccgccaucuucagcaaacccugaugaaggcuacaaag
uaagcgcaaguacccacguaaagacguuaggucaagguguagcccaugag
guggcaagaaaugggcuacauuuucuaccccagaaaacuacgauagcccu
uaugaaacuuaagggucgaagguggauuuagcaguaaacuaagaguagag
ugcuuaguugaacagggcccugaagcgcguacacaccgcccgucacccuc
cucaaguauacuucaaaggacauuuaacuaaaaccccuacgcauuuauau
agaggagacaagucguaacaugguaaguguacuggaaagugcacuuggac
gaa

mRNA 2:

gcuaaaccuagccccaaacccacuccaccuuacuaccagacaaccuuagc
caaaccauuuacccaaauaaaguauaggcgauagaaauugaaaccuggcg
caauagauauaguaccgcaagggaaagaugaaaaauuauaaccaagcaua
auauagcaaggacuaaccccuauaccuucugcauaaugaauuaacuagaa
auaacuuugcaaggagagccaaagcuaagacccccgaaaccagacgagcu
accuaagaacagcuaaaagagcacacccgucuauguagcaaaauaguggg
aagauuuauagguagaggcgacaaaccuaccgagccuggugauagcuggu
uguccaagauagaaucuuaguucaacuuuaaauuugcccacagaacccuc
uaaauccccuuguaaauuuaacuguuaguccaaagaggaacagcucuuug
gacacuaggaaaaaaccuuguagagagaguaaaaaauuuaacacccauag
uaggccuaaaagcagccaccaauuaagaaagcguucaagcucaacaccca
cuaccuaaaaaaucccaaacauauaacugaacuccucacacccaauugga
ccaaucuaucacccuauagaagaacuaauguuaguauaaguaacaugaaa
acauucuccuccgcauaagccugcgucagauuaaaacacugaacugacaa
uuaacagcccaauaucuacaaucaaccaacaagucauuauuacccucacu
gucaacccaacacaggcaugcucauaaggaaagguuaaaaaaaguaaaag
gaacucggcaaaucuuaccccgccuguuuaccaaaaacaucaccucuagc
aucaccaguauuagaggcaccgccugcccagugacacauguuuaacggcc
gcgguacccuaaccgugcaaagguagcauaaucacuuguuccuuaaauag
ggaccuguaugaauggcuccacgaggguucagcugucucuuacuuuuaac
cagugaaauugaccugcccgugaagaggcgggcauaacacagcaagacga
gaagacccuauggagcuuuaauuuauuaaugcaaacaguaccuaacaaac
ccacagguccuaaacuaccaaaccugcauuaaaaauuucgguuggggcga
ccucggagcagaacccaaccuccgagcaguacaugcuaagacuucaccag
ucaaagcgaacuacuauacucaauugauccaauaacuugaccaacggaac
aaguuacccuagggauaacagcgcaauccuauucuagaguccauaucaac
aauaggguuuacgaccucgauguuggaucaggacaucccgauggugcagc
cgcuauuaaagguucguuuguucaacgauuaaaguccuacgugaucugag
uucagaccggaguaauccaggucgguuucuaucuacnuucaaauuccucc
cuguacgaaaggacaagagaaauaaggccuacuucacaaagcgccuuccc
ccguaaaugauaucaucucaacuuaguauuauacccacacccacccaaga
acaggguu

tRNA list:

tRNA 1:

guuuauguagcuuaccuccucaaagcaauacacugaaaauguuuagacgg
gcucacaucaccccauaaac

tRNA 2:

cagaguguagcuuaacacaaagcacccaacuuacacuuaggagauuucaa
cuuaacuugaccgcucug

tRNA 3:

guuaagauggcagagcccgguaaucgcauaaaacuuaaaacuuuacaguc
agagguucaauuccucuucuuaac

tRNA 4:

agaaauaugucugauaaaagaguuacuuugauagaguaaauaauaggagc
uuaaacccccuuauuucu

tRNA 5:

cuaggacuaugagaaucgaacccaucccugagaauccaaaauucuccgug
ccaccuaucacaccccauccu

tRNA 6:

aguaaggucagcuaaauaagcuaucgggcccauaccccgaaaauguuggu
uauacccuucccguacu

tRNA 7:

agaaauuuagguuaaauacagaccaagagccuucaaagcccucaguaagu
ugcaauacuuaauuucu

tRNA 8:

uaaggacugcaaaaccccacucugcaucaacugaacgcaaaucagccacu
uuaauuaagcuaagcccu

tRNA 9:

cuagaccaaugggacuuaaacccacaaacacuuaguuaacagcuaagcac
ccuaaucaacuggcuucaaucu

tRNA 10:

aagccccggcagguuugaagcugcuucuucgaauuugcaauucaauauga
aaaucaccucggagc

tRNA 11:

ugguaaaaagaggccuaaccccugucuuuagauuuacaguccaaugcuuc
acucagccauuuuac

tRNA 12:

caaaaaaggaaggaaucgaaccccccaaagcugguuucaagccaacccca
uggccuccaugacuuuuu

tRNA 13:

aagguauuagaaaaaccauuucauaacuuugucaaaguuaaauuauaggc
uaaauccuauauaucuu

tRNA 14:

cacuguaaagcuaacuuagcauuaaccuuuuaaguuaaagauuaagagaa
ccaacaccucuuuacagug

tRNA 15:

acucuuuuaguauaaauaguaccguuaacuuccaauuaacuaguuuugac
aacauucaaaaaagagu

tRNA 16:

ugguauauaguuuaaacaaaacgaaugauuucgacucauuaaauuaugau
aaucauauuuacca

tRNA 17:

guaaauauaguuuaaccaaaacaucagauugugaaucugacaacagaggc
uuacgaccccuuauuuac

tRNA 18:

gagaaagcucacaagaacugcuaacucaugcccccaugucuaacaacaug
gcuuucuc

tRNA 19:

acuuuuaaaggauaacagcuauccauuggucuuaggccccaaaaauuuug
gugcaacuccaaauaaaagu

tRNA 20:

uauucucgcacggacuacaaccacgaccaaugauaugaaaaaccaucguu
guauuucaacuacaagaa

tRNA 21:

guccuuguaguauaaacuaauacaccagucuuguaaaccggagaugaaaa
ccuuuuuccaaggac

tRNA 22:

ucagagaaaaagucuuuaacuccaccauuagcacccaaagcuaagauucu
aauuuaaacuauucucu

Quantum Biology - 2

Close up of a virus brain?

I. Background

In a previous post I wrote that in a future post I would "do the math" related to the proton tunneling thingy (The Doll As Metaphor - 4). 

Doing even more preparation during the drum roll, I posted:

"Before you form a conclusion to answer the question, take a look at today's appendices (SARS-CoV-2 RNA with DNA nucleotide nomenclature; SARS-CoV-2 RNA with RNA nucleotide nomenclature) to see that a significant change should take place in nucleotide print outs.

Those two appendices detail the differences that should exist if DNA "thymine (T) [C₅H₆N₂O₂]" nomenclature was replaced with RNA "uracil (U) [C₄H₄N₂O₂]" nomenclature in the GenBank RNA virus records of the database."

(It's In The GenBank - 3). This hints at one reason virologists do not place a 'T' at the location in genome base pair sequences where a 'U' morpheme is the only morphology thingy that tells the truth.

II. Dicta

The SARS-CoV-2 virus, which is said to be the cause Covid-19, is an RNA virus, so, it does not have an A-T ('T' = thymine) base pair location, instead it has an A-U base pair location ('U' = uracil).

So, as I mentioned in "It's In The GenBank - 3" I converted 'T' to 'U' in the Wuhan sequenced genome (I learned in kindergarten that a 'T' is not a 'U' and I learned in high school that C₅H₆N₂O₂ 'T' thymine is not C₄H₄N₂O₂ 'U' uracil).

You can take a look at what the original Wuhan, China SARS-CoV-2 virus
looks like in improper DNA format and in proper RNA format at "It's In The GenBank - 3".

That post's appendices show the difference in the December 30, 2019 Wuhan, China collected SARS-CoV-2 virus (GenBank version "NC_045512.2") under the contrasting A-T vs A-U formats.

III. Do The Math

The A-U locations count in the SARS-CoV-2 virus genome is 1,238, the G-C locations count is 1,237, which totals to 2,475 locations per virus.

Do we revert to the teleonomy of playing with dolls to say "sometimes the virus 'savors' a genomic change and sometimes it doesn't" (The Misappropriation of Teleonomy)?

Or do we revert to "just the cold hard facts" to conclude that the hard science of probability indicates that this is a case where proton tunneling is quite a probable reality?

The Cornell University paper indicated:

"Furthermore, we find a large tautomeric occupation probability of 1.73 × 10⁻⁴, suggesting that such proton transfer may well play a far more important role in DNA mutation than has hitherto been suggested. Our results could have far-reaching consequences for current models of genetic mutations."

(An Open Quantum Systems approach to proton tunneling in DNA, Cornell University, September 2021, emphasis added). That research was based on one DNA A-T example, not the double RNA C-G A-U example.

Using both the C-G location and the A-U location in an RNA virus analysis seems quite likely to cut that Cornell University calculation in half or less (1.73 × 10⁻²).

Further, as I wrote years ago concerning the seminal Löwdin paper:

That "small but finite probability" gets much more probable by happening millions of repetitions per short amount of time (like a second or a minute) in the trillions of cells inside us.

(The Uncertain Gene). That is especially so when the "us" is the microbe hosts and their viruses within humans ("100 times more microbial genes than human genes" in humans).

III. Closing Comments

It is way past time to stop wondering "Why are RNA virus mutation rates so damn high" so we can, instead, have a Newtonian mechanics to Quantum Mechanics experience.

The next post in this series is here, the previous post in this series is here.