Quantum Biology - 14

Fig. 1 It's Around Here Somewhere

I. Background

In episode five of this series we looked in on classes at some ivy league universities and watched excellent portrayals of some of the dynamics of DNA and RNA (Quantum Biology - 5). 

Today we are going to look a bit deeper by asking whether or not all or some of the hypotheses related to those dynamics have been proven.

II. Faith and Trust?

What kind of belief, or trust, or science does it take to embrace or to falsify a hypothesis (The Pillars of Knowledge: Faith and Trust?)?

One answer advanced is "just the key of course":

"All of this is a hypothesis, proposed by John Sutherland, a chemist at the University of Cambridge in England. But he has tested all the required chemical reactions in a laboratory and developed evidence that they are plausible under the conditions expected of primitive Earth. Having figured out a likely chemistry needed to produce the starting materials of life, Dr. Sutherland then developed this geological scenario because it provides the conditions required by the chemistry. As for the chemistry itself, that springs from Dr. Sutherland’s discovery six years ago of the key to the RNA world."

(Making Sense of the Chemistry That Led to Life on Earth, emphasis added). Oh, "the key to the RNA world", not "a" key but "the" key?

One scientific "test" of a hypothesis, the test of its veracity, is whether or not it can be falsified (Falsifiability, cf. Karl Popper - Theory of Falsification).

III. What Was Required?

The initiator of a hypothesis is required to postulate how the hypothesis can be falsified (if "this", then it is falsified, otherwise it is workable):

"In common usage in the 21st century, a hypothesis refers to a provisional idea whose merit requires evaluation. For proper evaluation, the framer of a hypothesis needs to define specifics in operational terms. A hypothesis requires more work by the researcher in order to either confirm or disprove it. In due course, a confirmed hypothesis may become part of a theory or occasionally may grow to become a theory itself."

(ibid, Fig. 1 link). There are valid concerns that "the key to the RNA world" hypothesis does not meet the standard for a valid scientific hypothesis:

"Another reason why RNA catalysis is important lies in its postulated importance in the early development of life on the planet. It is the key to the RNA world hypothesis proposed by Crick, Orgel, and others that potentially solves a massive chicken-and-egg problem that results from the requirement for the coincident emergence of nucleic acids and proteins with a division of labor between genetic encoding and catalysis. While no-one can rewind the tape to prove such a scenario, the discovery of the peptidyl transferase ribozyme is the closest we get to a “smoking gun” proof of this concept. A viable RNA world would have required many more chemical activities than are represented by the currently-known ribozymes, and it is conceivable that 'molecular fossils' still exist." 

(RNA catalysis—is that it?, emphasis added). What would falsify the only key that can do it falsification is said to be a massive chicken-and-egg problem (which usually leads to playfulness: The Doll As Metaphor, 2, 3, 4, 5, 6, 7, 8).

One of the chicken-and-egg (which came first, this or that) problems is which came first DNA or RNA.

I mentioned DNA/RNA in Section I above, adding a link to the fifth episode of this series, which had a video of a DNA to mRNA transcription and translation.

That video is provided again at the bottom of this post.

IV. Onward to Eucaryotes

That video shows a transcription using the genome of a Eucaryote which is the type of cell we humans have ("A little high school biology review: Eukaryotes are cells with a nucleus and membrane-bound organelles, and they include fungal, plant and animal -- including human -- cells." Science Daily).

As the transcription & translation proceeds, notice that all of the nucleotides in the complimentary base pair ("C", "G", and "A") are copied, but the "T" complimentary base pair is not copied, instead it is converted into a "U".

I discussed that event in the post Some Of My Best Friends Are Germs, but that discussion did not include the Toxoplasma Gondii genome.

Today that issue is going to be discussed in the context of Eucaryotes because both human cells and Toxoplasma Gondii (see How To Identify The Despotic Minority - 16) cells are Eucaryotes (Note: that post quotes sources which point out that "Toxoplasmosis [Toxoplasma Gondii infection] is becoming a global health hazard as it infects 30–50% of the world human population").

V. Onward To Atoms

Today's appendices point out that the atoms in the DNA and RNA of Toxoplasma Gondii and humans do not add up to supporting "the key to the RNA world" that has been discussed earlier in this post.

Thus, the atomic reality should also be a part of the test as to the hypothesis of John Sutherland, Crick, Orgel, and others mentioned earlier in this post, who are said to have proven "the key to the RNA world" hypothesis.

Again, one reason for this is that the atomic structure of "T" (Thymine) is not the same as the atomic structure of "U" (Uracil):

"The appendices to today's post show mutant codons (Appendix One) and the differences in atom counts (Appendix Two) in one nucleotide of DNA (T,  thymine) compared to the relevant nucleotide of RNA (U, uracil).

The codons and amino acids related to mRNA (mRNA codons have "U" instead of "T") in the lines of Appendix Two follow (are on the following line) the codons of the lines of DNA codons.

This (Appendix Two) shows that the atom counts in DNA 'T' do not match the atom counts of RNA 'U' ('T' parts are not 'U' parts).

Considerable skill is required to move atoms out of or into a molecule, yet that happens during DNA -> mRNA transcription (see videos below).

As it were, one carbon atom and two hydrogen atoms are removed from 'T' which results in 'U' during codon transcription processing.

As you can see in those appendices, this is done in the cells of eucaryotes millions and millions of times daily."

(Quantum Biology - 5, at section "II. Appendices", cf. Quantum Biology, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13).

Fig. 2 by Celeste Roberge

There's nothing left to do but count the atoms, which like rocks (Fig. 2), don't change what they are just because we put them in a large pile (Small Brains Considered - 11). 

VI. Closing Comments

As if that was not enough, those scientists who have become intellectually adrift go even further.

Yes, there are even some once quantum physics based scientists who have, in effect then, indicated that the secrets of the Eastern Mystical Religions and the Western Christian Religions are hidden deep in the, "as it were", pile of rocks (Small Brains Considered - 7).

This Dr. Falkowski video below addresses "we don't know":

Dr. Paul Falkowski

"Andy. Thank you very much, Andy, and thanks for inviting me here. It's a pleasure. So 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. Falkowski

(From the transcript, emphasis added).

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

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A tale of two other brain areas (one in the nucleus, the other in the ribosomes)?:

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