In a paper published in Nature magazine: Searching for lost nucleotides of the pre-RNA World, published in 2018
the authors claim: There may have been different nucleotides, and many more of them, on the prebiotic Earth than are found in extant RNA. 1
The nucleotides of RNA appear to be products of evolution.
Question: How do they know this ?
The origin of the first nucleotides and the origin of RNA are related open questions
My comment: Nice confession
There may have been different nucleotides, and many more of them, on the prebiotic Earth than are found in extant RNA. There could have been a wide variety of molecular building blocks. With this freedom comes the liability of becoming lost in the vast chemical space of possible prebiotic molecules without ever finding the nucleotides that initiated the march toward RNA.
My comment: That means, in order to have the nucleotides with the four nucleobases, adenine, guanine, cytosine, uracil, and later, in DNA thymine, used in life, these useful ones would have to be selected out amongst all the different ones that could have existed and occurred naturally on earth. There was however no such chemical evolution or selection process. The question is: If that is so, how do the authors attempt to explain a prebiotic selection process to sort out the functional nucleotides, and the four bases, used in life? And why would natural processes do such a selection, in face of the fact, that there is no reason why that should occur.
Uncovering the origins of nucleotides and genetic polymers requires understanding the various chemical reactions that produce such molecules
My comment: Indeed. And the outcome had to be the production of the four RNAs used in life, with the four bases, exclusively and joining them in sufficient quantity at the same building site. Since the smallest known genome, mycoplasma genitalum, uses 580 thousand nucleotides, and anything less would not generate a living cell, at least this quantity would have had to be united and joined together.
The RNA-first proponents are limited by the chemical stability, reactivity, and functionality of the molecular subunits that comprise the extant nucleotides. Consequently, the RNA-first proponents must, understandably, sometimes rely on specific minerals (e.g., borate) or geological events (e.g., meteorite impacts) to control, guide, or initiate a particular reaction or reaction sequence.
My comment: Meteorite impacts are chaotic. How can chaotic events control anything? In order to have a functional minimal information-bearing genome, RNA and DNA nucleotide monomers are required. To get functional ones, you need to sort them out between left-handed and right-handed nucleotide configurations ( the homochirality problem). Only right-handed nucleotides are used in cells. There is no selection process known besides the one used in cells by sophisticated enzymes, which produce only right-handed nucleotides.
The chemical structure of the extant RNA nucleotides is modular, with each nucleotide containing three molecular subunits: phosphate, ribose and a nucleobase. This general structure has long inspired chemists to hypothesize that the subunits were formed separately on the early Earth
My comment: There are many problems with this hypothesis, and they are persistent, and unsolved. High-energy precursors to produce purines and pyrimidines would have had to be produced in a sufficiently concentrated form. There is no known prebiotic route to this. The best-studied mechanism relevant to the prebiotic synthesis of ribose is the formose reaction. Several problems have been recognized for the ribose synthesis via the formose reaction. The formose reaction is very complex. It depends on the presence of a suitable inorganic catalyst. Ribose is merely an intermediate product among a broad suite of compounds including sugars with more or fewer carbons. There would have been no way to activate phosphate somehow, in order to promote the energy dispendious reaction.
....and subsequently joined together by dehydration condensation reactions. That is, both the bond connecting phosphate to ribose and the bond between ribose and the nucleobase release a water molecule as they are formed.
My comment: In order a molecule to be a self-replicator, it has to be a homopolymer, of which the backbone must have the same repetitive units; they must be identical. In the prebiotic world, the generation of a homopolymer was however extremely unlikely, if not impossible. The activated nucleotides (or the nucleotides with coupling agent) now had to be polymerized. In the case of RNA, not only must phosphodiester links be repeatedly forged, but they must ultimately connect the 5 prime‑oxygen of one nucleotide to the 3 prime‑oxygen, and not the 2 prime‑oxygen, of the next nucleotide. . How could and would random events attach a phosphate group to the right position of a ribose molecule to provide the necessary chemical activity?
The coupling of each nucleotide to a growing RNA polymer also generates a water molecule
My comment: Water is commonly viewed as essential for life, and theories of water are well known to support this as a requirement. So are RNA, DNA, and proteins. However, these biopolymers are corroded by water. For example, the hydrolytic deamination of DNA and RNA nucleobases is rapid and irreversible, as is the base-catalyzed cleavage of RNA in water. This leads to a paradox: RNA requires water to do its job, but RNA cannot emerge in water and cannot replicate with sufficient fidelity in water without sophisticated repair mechanisms in place. There are no solutions in sight to solve this paradox; life needs water that is inherently toxic to RNA necessary for life.
Biological Cells are irreducibly complex:
1. Cell subunits and compartments form a complex system that is useful only in the completion of a much larger system that is able to keep the basic functions of life. A minimal Cell, in order to permit life, according to an article in Science magazine, from 2016, requires a minimal genome of about 473gene products, and at least 438 proteins, each fully set up and functional for specific tasks. A discrete minimal size of each individual protein complex formed by multiple subunits and cofactors is required in order to be functional. And it only operates when interconnected and in a joint venture similar to a robot in a production line, and precise energy supply.
2. Cells must be created and be functional, all at once. As Graham Cairns-Smith noted, this system has to be fixed in its essentials through the critical interdependence of subsystems. Irreducibly complex and interdepend systems cannot evolve but depend on intelligence with foreknowledge on how to build discrete parts with distant goals.
3. Therefore, intelligent design is the best explanation of the origin of living, self-replicating cells.
There is no feasible prebiotic naturalistic unguided route to nucleotide synthesis. And even IF that were the case: These nucleotides would have to be joined in the right order to produce functional instructional information. But even IF that would be the case, what good would there be for a genome without the machinery to transcribe, and translate the information, to produce functional proteins? And even IF that would be the case, what good would functional proteins be good for, if not transported to the right site in the Cell, inserted in the right place, and interconnected to start the fabrication of chemical compounds used in the Cell? It is clear, that life had to start based on fully operating cell factories, able to self replicate, adapt, produce energy, regulate its sophisticated molecular machinery.
RNA & DNA: It's prebiotic synthesis: Impossible !!
RNA & DNA: It's prebiotic synthesis: Impossible !! Part 1
RNA & DNA: It's prebiotic synthesis: Impossible !! Part 2
Last edited by Admin on Mon Jul 06, 2020 9:44 am; edited 4 times in total