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| DNA is mostly (Space) |
This series contains subject matter that has a long history here on Dredd Blog.
A large part of the discussion deals with biologists who recoil at the mention of the time prior to 'bio' when there was only 'abio'.
For example (Putting A Face On Machine Mutation - 3; The Life and Death of Bright Things; Did Abiotic Intelligence Precede Biotic Intelligence?; Weekend Rebel Science Excursion - 27, If Cosmology Is "Off," How Can Biology Be "On?", 2, 3) to name a few.
II. Now
The purpose of this series is to point out that photons, electrons, protons, and neutrons are not biotic, they are abiotic.
However, since biologists expound upon DNA and RNA incessantly without giving sufficient credit to the "little ones", i.e., the quantum realm of atoms and molecules that perform according to the laws of physics, i.e., quantum mechanics (Quantum Biology, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19), so I have complained incessantly about it:
"The better part of a decade ago Dredd Blog was complaining about a non-existent science called "Abiology" that should exist (Weekend Rebel Science Excursion - 27, quoting Dredd Blog posts from 2012)."
(First post of this series). People may wonder "who are you to complain about this" to which I will reply "who am I not to complain about it"?
III. A Remarkable Picture
The two appendices to today's post point out the quantum dynamics that our text books, for the most part, are ignoring (Quantum DNA, Quantum RNA).
Before we continue in this post, I might be remiss if I did not point out that I have mentioned a professor, a scientist who has covered the abiotic realm quite succinctly:
"I just want to begin this by thinking about a bridge. In this particular case, it's an obvious bridge. And if you think about evolution, you know where we've come to, but you don't know where we began. So origins of life is one of the most challenging problems facing science. Actually, as my friend and colleague Nick Lane says, it's the black hole of science. It's an embarrassment. And it's a very complicated problem."
(Dr. Paul Falkowski, YouTube). Anyway, on to the quanta.
IV. The Nonliving Atomic Scientists
Biology has a "central dogma" which once upon a time was paraphrased as "RNA comes from DNA" (NCBI).
You can view it visually and audibly in the videos at the end of today's post.
But before that, let's get down to the nitty gritty and follow the atoms instead of just following the base pairs (a.k.a. nucleotides).
Let's follow the trail of the atomic footprint of some DNA/RNA codons from a gene through transcription to mRNA then on to the ribosome where it is reformed into an amino acid:
The appendices show that the codon "GCT" (Guanine [C5H5N5O1], Cytosine[C4H5N3O1], Thymine [C5H6N2O2]) while in the DNA strand becomes "GCU" (Guanine [C5H5N5O1], Cytosine [C4H5N3O1], and Uracil [C4H4N2O2]) during transcription, as shown in the first video at the end of this post.
In other words, as shown in the DNA Appendix, [C14H16N10O4] becomes [C13H14N10O4].
This
is "atomic surgery" that removes 1 Carbon atom, and two Hydrogen atoms
from the GCT codon molecular structure to produce GCU (i.e. 'Thymine' is converted into 'Uracil', with 3 atoms left over).
No human brain surgeon can do that, but it is happening millions of times a second in us at all times.
Next,
the nucleus (of the cell where the mRNA was transcribed from DNA) then sends
that mRNA out of the nucleus into the cytoplasm outside of the nucleus.
There a ribosome will do more atomic surgery so as to "carve out" the
amino acid Alanine [C3H7N1O2] from the GCU codon [C13H14N10O4].
Evidently some atoms will be "left over" (like when I assemble things I ordered and received in the mail ... got leftover parts?).
That
is, 13-3 = 10, 14-7 = 7, 10-1 = 9, and 4-2 = 2; hence 10 carbon, 7
hydrogen, 9 nitrogen, and 2 oxygen atoms are "left over" when the ribosome
converts GCU into Alanine.
Now, go down the list of amino acids in
the two appendices, and add up the "left over" atoms, and one wonders if
the left overs are used on the next translation from codon to amino
acid.
Perhaps biologists don't like to talk about this because,
as Dr. Falkowski pointed out (Section III above), it is a part of the black hole of
genetics, akin to the "black hole" made famous or infamous by cosmologists.
How the "macromolecular machines" called 'ribosomes' became atomic surgeons is indeed another one of the many black holes of our scientific knowledge.
V. Closing Comments
The essences I am getting at is that when we are asked to take "central dogma" on faith or trust, that is not going to educate us, instead it is going to indoctrinate us (The Pillars of Knowledge: Faith and Trust?).
The next post in this series is here, the previous post in this series is here.
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