RNA & DNA: It's prebiotic synthesis: Impossible !!

RNA & DNA: It's prebiotic synthesis: Impossible !!

https://reasonandscience.catsboard.com/t2865-rna-dna-it-s-prebiotic-synthesis-impossible

RNA & DNA: It's prebiotic synthesis: Impossible !! Part 1
https://www.youtube.com/watch?v=-ZFlmL_BsXE

RNA & DNA: It's prebiotic synthesis: Impossible !! Part 2
https://www.youtube.com/watch?v=dv4mUjmuRRU

Main points addressed in the video
Synthesis of nitrogenous bases in prebiotic environments
- 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.  
- Scientists have failed to produce cytosine in spark-discharge experiments, nor has cytosine been recovered from meteorites or extraterrestrial sources. The deamination of cytosine and its destruction by other processes such as photochemical reactions place severe constraints on prebiotic cytosine syntheses.
- The origin of guanine bases has proven to be a particular challenge. While the other three bases of RNA  could be created by heating a simple precursor compound in the presence of certain naturally occurring catalysts, guanine had not been observed as a product of the same reactions.
- Adenine synthesis requires unreasonable Hydrogen cyanide concentrations. Adenine deaminates 37°C with a half-life of 80 years. Therefore, adenine would never accumulate in any kind of "prebiotic soup." The adenine-uracil interaction is weak and nonspecific, and, therefore, would never be expected to function in any specific recognition scheme under the chaotic conditions of a "prebiotic soup."
- Uracil has also a half-life of only 12 years at 100◦C. For nucleobases to accumulate in prebiotic environments, they must be synthesized at rates that exceed their decomposition.
Ribose: Synthesis problems of the Pentose 5 carbon sugar ring
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.
The phosphate group

On prebiotic earth, however, there would have been no way to activate phosphate somehow, in order to promote the energy dispendious reaction.

Prebiotic RNA and DNA synthesis
1. No prebiotic mechanism is known to select:
- Right-handed configurations of RNA and DNA
- The right backbone sugar
- How to get size complementarity of the nucleotide bases to form a DNA strand and strands of the DNA molecule running in the opposite directions
2. Bringing all the parts together and joining them in the right position
- Attach the nucleic bases to the ribose and in a repetitive manner at the same, correct place, and the backbone being a repetitive homopolymer
- Prebiotic glycosidic bond formation between nucleosides and the base
- Prebiotic phosphodiester bond formation
- Fine-tuning of the strength of the hydrogen base pairing forces
3. The instability, degradation, and asphalt problem
- Bonds that are thermodynamically unstable in water, and overall intrinsic instability. RNA’s nucleotide building blocks degrade at warm temperatures in time periods ranging from nineteen days to twelve years. These extremely short survival rates for the four RNA nucleotide building blocks suggest why life’s origin would have to be virtually instantaneous—all the necessary RNA molecules would have to be assembled before any of the nucleotide building blocks decayed.
4. The energy problem
- Doing things costs energy. There has to be a ready source of energy to produce RNA. In modern cells, energy is consumed to make RNA.
5. The minimal nucleotide quantity problem.
- The prebiotic conditions would have had to be right for reactions to give perceptible yields of bases that could pair with each other.
6. The Water Paradox  
- 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.
7.The transition problem from prebiotic to biochemical synthesis
- Even if all this in a freaky accident occurred by random events, that still says nothing about the huge gap and enormous transition that would be still ahead to arrive at a fully functional interlocked and interdependent metabolic network, where complex biosynthesis pathways produce nucleotides in modern cells.
Unguided prebiotic synthesis of RNA and DNA: an unsolved riddle!

I think, to say that on average the 14 hurdles that it would take to make primed nucleotides would each take 10 unit operations - that at least 140 little events would have to be appropriately sequenced. Unguided, the appropriate thing happened at each point on one occasion in six.The odds against a successful unguided synthesis of a batch of primed nucleotide on the primitive Earth would be a huge number, represented approximately by a 1 followed by 109 zeros ( 10^109). 'The odds are enormous against its being coincidence. No figures could express them.'

Synthesis of nitrogenous bases in prebiotic environments
- 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.  
- Scientists have failed to produce cytosine in spark-discharge experiments, nor has cytosine been recovered from meteorites or extraterrestrial sources. The deamination of cytosine and its destruction by other processes such as photochemical reactions place severe constraints on prebiotic cytosine syntheses.
- The origin of guanine bases has proven to be a particular challenge. While the other three bases of RNA  could be created by heating a simple precursor compound in the presence of certain naturally occurring catalysts, guanine had not been observed as a product of the same reactions.
- Adenine synthesis requires unreasonable Hydrogen cyanide concentrations. Adenine deaminates 37°C with a half-life of 80 years. Therefore, adenine would never accumulate in any kind of "prebiotic soup." The adenine-uracil interaction is weak and nonspecific, and, therefore, would never be expected to function in any specific recognition scheme under the chaotic conditions of a "prebiotic soup."
- Uracil has also a half-life of only 12 years at 100◦C. For nucleobases to accumulate in prebiotic environments, they must be synthesized at rates that exceed their decomposition.

Ribose: Synthesis problems of the Pentose 5 carbon sugar ring
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.

The phosphate group
On prebiotic earth, however, there would have been no way to activate phosphate somehow, in order to promote the energy dispendious reaction.

1. No prebiotic mechanism is known to select: 
- Right-handed configurations of RNA and DNA
- The right backbone sugar
- How to get size complementarity of the nucleotide bases to form a DNA strand and strands of the DNA molecule running in the opposite directions

2. Bringing all the parts together and joining them in the right position 
- Attach the nucleic bases to the ribose and in a repetitive manner at the same, correct place, and the backbone being a repetitive homopolymer
- Prebiotic glycosidic bond formation between nucleosides and the base
- Prebiotic phosphodiester bond formation
- Fine-tuning of the strength of the hydrogen base pairing forces

3. The instability, degradation, and asphalt problem 
- Bonds that are thermodynamically unstable in water, and overall intrinsic instability. RNA’s nucleotide building blocks degrade at warm temperatures in time periods ranging from nineteen days to twelve years. These extremely short survival rates for the four RNA nucleotide building blocks suggest why life’s origin would have to be virtually instantaneous—all the necessary RNA molecules would have to be assembled before any of the nucleotide building blocks decayed.

4. The energy problem
- Doing things costs energy. There has to be a ready source of energy to produce RNA. In modern cells, energy is consumed to make RNA.

5. The minimal nucleotide quantity problem.
- The prebiotic conditions would have had to be right for reactions to give perceptible yields of bases that could pair with each other.

6. The Water Paradox  
- 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.

7.The transition problem from prebiotic to biochemical synthesis 
- Even if all this in a freaky accident occurred by random events, that still says nothing about the huge gap and enormous transition that would be still ahead to arrive at a fully functional interlocked and interdependent metabolic network, where complex biosynthesis pathways produce nucleotides in modern cells.

Synthesis of nitrogenous bases in prebiotic environments
- 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.  
- Scientists have failed to produce cytosine in spark-discharge experiments, nor has cytosine been recovered from meteorites or extraterrestrial sources. The deamination of cytosine and its destruction by other processes such as photochemical reactions place severe constraints on prebiotic cytosine syntheses.
- The origin of guanine bases has proven to be a particular challenge. While the other three bases of RNA  could be created by heating a simple precursor compound in the presence of certain naturally occurring catalysts, guanine had not been observed as a product of the same reactions.
- Adenine synthesis requires unreasonable Hydrogen cyanide concentrations. Adenine deaminates 37°C with a half-life of 80 years. Therefore, adenine would never accumulate in any kind of "prebiotic soup." The adenine-uracil interaction is weak and nonspecific, and, therefore, would never be expected to function in any specific recognition scheme under the chaotic conditions of a "prebiotic soup."
- Uracil has also a half-life of only 12 years at 100◦C. For nucleobases to accumulate in prebiotic environments, they must be synthesized at rates that exceed their decomposition.

Ribose: Synthesis problems of the Pentose 5 carbon sugar ring
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.

The phosphate group
On prebiotic earth, however, there would have been no way to activate phosphate somehow, in order to promote the energy dispendious reaction.

Unguided prebiotic synthesis of RNA and DNA: an unsolved riddle!
The origin of the RNA and DNA molecule is an origin of life problem, not evolution.
Steve Benner, one of the world’s leading authorities on abiogenesis:  The “origins problem” CANNOT be solved.
Graham Cairns-Smith: The odds against a successful unguided synthesis of a batch of primed nucleotide on the primitive Earth would be a huge number, represented approximately by a 1 followed by 109 zeros ( 10^109). 'The odds are enormous against its being coincidence. No figures could express them.'

Tan, Change; Stadler, Rob. The Stairway To Life
The longest chains (up to fifty monomers) and the highest production of molecules with the correct bonds have been achieved in the presence of montmorillonite clay. With purine nucleotides (adenosine and guanine), the percentage of correct phosphodiester bonds actually exceeded that of the incorrect bonds. However, the addition of each monomer to the chain comes with a probability of incorrect bonding, and one incorrect bond irreversibly destroys the homolinkage of the growing polymer, just as a train with one derailed boxcar can destroy the entire train. Therefore, the synthetic yield of biopolymers with the desired homolinkage decreases exponentially as the length of the biopolymer increases—even when starting only with pure building blocks.

In the presence of montmorillonite, polymerization of purine nucleotides (i.e., adenine and guanine) is favored over pyrimidine nucleotides (i.e., cytosine, thymine, and uracil) . This would constrain the potential information-carrying capacity of the resulting polymers, somewhat like requiring an author to have the letters A through M appear in their writing twice as often as the letters N through Z.

Another issue with the montmorillonite-catalyzed reaction is that the most successful polymerization occurred with an inosine nitrogenous base, which is not used to synthesize natural DNA or RNA. Also, the resulting oligomers decompose in the presence of water and the clay accelerates this decomposition.

Production of DNA with perfect homolinkage throughout the length of a genome (for example, there are approximately 500,000 nucleotides in the simplest known free-living organism’s genome) is impossible without the molecular machinery that is available only in living organisms.

An E. coli cell is about two micrometers long (two millionths of a meter) and one micrometer in diameter, and it contains a circular DNA molecule with 4.6 million base pairs. If fully extended, the DNA molecule would measure about 1.4 millimeters, or about 700 times longer than the E. coli cell. Picture your car, representing an E. coli, containing a rope that represents the DNA. Scaling up the E. coli to become the size of your car (about five meters or sixteen feet in length), the DNA would correspondingly scale up to approximately 3.5 kilometers or 2.2 miles of rope with a diameter of six millimeters or ¼ inch, contained in your car. Indeed, all of that DNA has to be compressed to fit within each bacterial cell. Now, imagine the E. coli cell duplicating this DNA before replication and needing to separate the two interlinked copies before cell division. Genomic DNAs are so long that they cannot fit into any cells without being highly compacted with the help of multiple proteins. Also, such a length of rope cannot be manipulated without kinking and supercoiling, especially when DNA is unwound for reproduction. Additional topoisomerase enzymes and structural maintenance of chromosome (SMC) proteins are essential for this purpose.

Prof. Steven A. Benner: When Did Life Likely Emerge on Earth in an RNA-First Process? 24 September 2019
All of these path‐hypotheses involve relatively reduced organic molecules that serve as the precursors of the four standard RNA nucleobases (guanine, adenine, cytosine, and uracil) or “grandfather′s axe” heterocycles (not shown). Thus, all assume the production of substantial amounts of reduced primary precursors, likely in the Hadean atmosphere (before 4 billion years ago). These primary precursors include hydrogen cyanide (HCN), cyanamide (H2NCN), cyanoacetylene (HCCCN), cyanogen (NCCN), ammonia (NH3), and cyanic acid (HCNO). Further, they all assume that these (or their downstream products) avoided dilution into a global ocean, perhaps by adsorbing on solids, or by delivery to sub‐aerial land with a constrained aquifer. Most chemical path‐hypotheses to create RNA prebiologically all but require an atmosphere that is more reducing than what planetary accretion models suggest was the norm above the Hadean Earth.
https://chemistry-europe.onlinelibrary.wiley.com/doi/full/10.1002/syst.201900035

Prof. Steven A. Benner: Asphalt, Water, and the Prebiotic Synthesis of Ribose, Ribonucleosides, and RNA 2012
Some bonds in RNA appear to be “impossible” to form under any conditions considered plausible for early Earth
https://pubs.acs.org/doi/abs/10.1021/ar200332w

Henderson James Cleaves: One Among Millions: The Chemical Space of Nucleic Acid-Like Molecules  September 9, 2019
Various types of nucleic acid-like molecules have been enumerated and synthesized, but this is the first systematic attempt to enumerate, quantify and describe this chemical space. This space is surprisingly large, though its size appears predictable by typical isomerism studies. It is remarkable, given the existence of this structure space, that biology found a solution to the need for information storage. Is the solution life found to genetic molecular information storage optimal? In one sense obviously yes: it works very well and has managed to robustly support biological evolution over 3.5-4 Ga of planetary change. In another sense, from the standpoint of xeno- and synthetic biology, could other, perhaps equally good, or even better genetic systems be devised? The answer to this question will require sophisticated and protracted chemical experimentation. Studies to date suggest that the answer could be no. Many nearly as good, some equally good, and a few stronger base-pairing analogue systems are known.
https://pubs.acs.org/doi/10.1021/acs.jcim.9b00632

Graham Cairns-Smith: Genetic takeover,  page 66:
Now you may say that there are alternative ways of building up nucleotides, and perhaps there was some geochemical way on the early Earth. But what we know of the experimental difficulties in nucleotide synthesis speaks strongly against any such supposition. However it is to be put together, a nucleotide is too complex and metastable a molecule for there to be any reason to expect an easy synthesis. If you were to consider in more detail a process such as the purification of an intermediate ( to form amide bonds between amino acids and nucleotides ) you would find many subsidiary operations — washings, pH changes and so on. (Remember Merrifield’s machine: for one overall reaction, making one peptide bond, there were about 90 distinct operations required.)
https://3lib.net/book/2797668/0495a0

A. Graham Cairns-Smith: Chemistry and the Missing Era of Evolution 
What is missing from this story of the evolution of life on earth is the original means of producing such sophisticated materials as RNA. The main problem is that the replication of RNA depends on a clean supply of rather complicated monomers—activated nucleotides. What was required to set the scene for an RNA world was a highly competent, long-term means of production of at least two nucleotides. In practice the discrimination required to make nucleotide parts cleanly, or to assemble them correctly, still seems insufficient.
https://sci-hub.ren/10.1002/chem.200701215

Let us consider some of the difficulties to make RNA & DNA
1. as we have seen, it is not even clear that the primitive Earth would have generated and maintained organic molecules. All that we can say is that there might have been prevital organic chemistry going on, at least in special locations. 
2. highenergy precursors of purines and pyrimidines had to be produced in a sufficiently concentrated form (for example at least 0.01 M HCN). 
3. the conditions must now have been right for reactions to give perceptible yields of at least two bases that could pair with each other. 
4. these bases must then have been separated from the confusing jumble of similar molecules that would also have been made, and the solutions must have been sufficiently concentrated. 
5. in some other location a formaldehyde concentration of above 0.01 M must have built up. 
6. this accumulated formaldehyde had to oligomerise to sugars. 
7. somehow the sugars must have been separated and resolved, so as to give a moderately good concentration of, for example, D-ribose. 
8. bases and sugars must now have come together. 
9. Ninth, they must have been induced to react to make nucleosides. (There are no known ways of bringing about this thermo dynamically uphill reaction in aqueous solution: purine nucleosides have been made by dry phase synthesis, but not even this method has been successful for condensing pyrimidine bases and ribose to give nucleosides
10. Whatever the mode of joining base and sugar it had to be between the correct nitrogen atom of the base and the correct carbon atom of the sugar. This junction will fix the pentose sugar as either the a- or fl-anomer of either the furanose or pyranose forms. For nucleic acids it has to be the fl-furanose. (In the dry-phase purine nucleoside syntheses referred to above, all four of these isomers were present with never more than 8 ‘Z, of the correct structure.) 
11. phosphate must have been, or must now come to have been, present at reasonable concentrations. (The concentrations in the oceans would have been very low, so we must think about special situations—evaporating lagoons and such things  
12. the phosphate must be activated in some way — for example as a linear or cyclic polyphosphate — so that (energetically uphill) phosphorylation of the nucleoside is possible. 
13. to make standard nucleotides only the 5’- hydroxyl of the ribose should be phosphorylated. (In solid-state reactions with urea and inorganic phosphates as a phosphorylating agent, this was the dominant species to begin with. Longer heating gave the nucleoside cyclic 2’,3’-phosphate as the major product although various dinucleotide derivatives and nucleoside polyphosphates are also formed 
14. if not already activated — for example as the cyclic 2’,3’-phosphate — the nucleotides must now be activated (for example with polyphosphate) and a reasonably pure solution of these species created of reasonable concentration. Alternatively, a suitable coupling agent must now have been fed into the system. 
15. the activated nucleotides (or the nucleotides with coupling agent) must now have polymerised. Initially this must have happened without a pre-existing polynucleotide template (this has proved very difficult to simulate ; but more important, it must have come to take place on pre-existing polynucleotides if the key function of transmitting information to daughter molecules was to be achieved by abiotic means. This has proved difficult too. Orgel & Lohrmann give three main classes of problem. 
(i) While it has been shown that adenosine derivatives form stable helical structures with poly(U) — they are in fact triple helixes — and while this enhances the condensation of adenylic acid with either adenosine or another adenylic acid — mainly to di(A) - stable helical structures were not formed when either poly(A) or poly(G) Were used as templates. 
(ii) It was difficult to find a suitable means of making the internucleotide bonds. Specially designed water-soluble carbodiimides were used in the experiments described above, but the obvious pre-activated nucleotides — ATP or cyclic 2’,3’-phosphates — were unsatisfactory. Nucleoside 5'-phosphorimidazolides, for example: N/\ n K/N/P-r’o%OHN/\N were more successful, but these now involve further steps and a supply of imidazole, for their synthesis. 
(iii) Internucleotide bonds formed on a template are usually a mixture of 2’—5’ and the normal 3’—5’ types. Often the 2’—5’ bonds predominate although it has been found that Zn“, as well as acting as an eflicient catalyst for the templatedirected oligomerisation of guanosine 5’-phosphorimidazolide also leads to a preference for the 3’—5’ bonds. 
16. the physical and chemical environment must at all times have been suitable — for example the pH, the temperature, the M2+ concentrations. 
17. all reactions must have taken place well out of the ultraviolet sunlight; that is, not only away from its direct, highly destructive effects on nucleic acid-like molecules, but away too from the radicals produced by the sunlight, and from the various longer lived reactive species produced by these radicals. 
18. unlike polypeptides, where you can easily imagine functions for imprecisely made products (for capsules, ionexchange materials, etc), a genetic material must work rather well to be any use at all — otherwise it will quickly let slip any information that it has managed to accumulate. 
19. what is required here is not some wild one-off freak of an event: it is not true to say ‘it only had to happen once’. A whole set-up had to be maintained for perhaps millions of years: a reliable means of production of activated nucleotides at the least.

As the difficulties accumulate the stakes get higher: success would be all the more resounding, but it becomes less likely. Sooner or later it becomes wiser to put your money elsewhere.



Richard Van Noorden:  RNA world easier to make 13 May 2009
Although Sutherland has shown that it is possible to build one part of RNA from small molecules, objectors to the RNA-world theory say the RNA molecule as a whole is too complex to be created using early-Earth geochemistry. "The flaw with this kind of research is not in the chemistry. The flaw is in the logic — that this experimental control by researchers in a modern laboratory could have been available on the early Earth," says Robert Shapiro
Shapiro sides with supporters of another theory of life's origins – that because RNA is too complex to emerge from small molecules, simpler metabolic processes, which eventually catalysed the formation of RNA and DNA, were the first stirrings of life on Earth. Sutherland, though, hopes that ingenious organic chemistry might provide an RNA synthesis so convincing that it effectively serves as proof. "We might come up with something so coincidental that one would have to believe it," he says. "That is the goal of my career."
https://www.nature.com/articles/news.2009.471

Robert Shapiro: Life: What A Concept! 2008

SHAPIRO: Since then, so-called prebiotic chemistry, which is of course falsely named, because we have no reason to believe that what they're doing would ever lead to life — I just call it 'investigator influenced abiotic organic chemistry' — has fallen into the same trap. In the proceedings of the National Academy of Sciences about two months ago there was a paper — I think it was theoretical — they showed that in certain hydro-thermal events, convection forces and other attractive forces, about which I am unable to comment, would serve to concentrate organic molecules, so that organic molecules would get much more concentrated in the bottom of this than they would in the ordinary ocean. Very nice, perhaps it's a good place for the origin of life, and interesting finding, but then there was another commentary paper in the Proceedings by another invited commentator, who said, Great advance for RNA world because if you put nucleotides in, they'll be concentrated enough to form RNA; and if you put RNA in, the RNA will come together and form aggregates, giving you much more chance of forming a ribosome or whatever. I looked at the paper and thought, How did nucleotides come in? How did RNA come in? How did anything come in? The point is, you would take whatever mess prebiotic chemistry gives you and you would concentrate that mess so it's relevant to RNA or the origin of life — it's all in the eye of the beholder. And almost all of prebiotic chemistry is like this; they take chemicals of their own selection.

People were talking about Steve Benner and his borate paper where he selected, of his own free will, the chemical formaldehyde, the chemical acid-aldehyde, and the mineral borate, and he decided to mix them together and got a product that he himself said was significant in leading to the origin of RNA world, and I, looking at the same thing, see only the hands of Steve Benner reaching to the shelf of organic chemicals, picking formaldehyde, and from another shelf, picking acidaldehyde, etc. Excluding them carefully. Picking a mineral which occurs only in selective places on the Earth and putting it in in heavy doses. And at the end getting a complex of ribose and borate, which by itself would be of no use for making RNA, because the borate loves to hold onto the ribose, and as long as it holds onto the ribose it can't be used to make RNA. If it lets go of the ribose, then the ribose becomes vulnerable to destruction by all the other environmental agents. The half-life of pure ribose in solution, a different experiment and a very good one, by Stanley Miller is of the order of one or two hours, and all of the other sugars prominent in Earth biology have similar instability.

I was publishing papers like this and I got the reputation, or the nickname in the laboratory of the prebiotic chemist, of 'Dr. No'. If someone wanted a paper murdered, send it to me as a referee. And so on. At some point, someone said, Shapiro, you've got to be positive somewhere. So how did life start? And do we have any examples of authentic abiotic chemistry, not subject to investigator interference? The only true samples we have are those meteorites, which are scooped up quickly and often fallen in an unspoiled place — there was a famous meteorite that fell in France in a sheep field in the 1840s and led to dreadful chemistry of people seeing all sorts of bio molecules in it, not surprisingly. But if you took pristine meteorites and look inside, what you see are a predominance of simple organic compounds. The smaller the organic compound, the more likely it is to be present. The larger it is, the less likely it is to be present. Amino acids, yes, but the simplest ones. Over a hundred of them. All the simplest ones, some of which, coincidentally, overlap the unique set of 20 that coincide with Earth life, but not
containing the larger amino acids that overlap with Earth life. And no sample of a nucleotide, the building block of RNA or DNA, has ever been discovered in a natural source apart from Earth life. Or even take off the phosphate, one of the three parts, and no nucleoside has ever been put together. Nature has no inclination whatsoever to build nucleosides or nucleotides that we can detect, and the pharmaceutical industry has discovered this.

Life had to start with the mess — a miscellaneous mixture of organic chemistry to begin with. How do you organize this? You have to have a preponderance of some chemicals or lacking others would be against the second law of thermo-dynamics — it violates a concept that as a non-physicist that I barely grasp called 'entropy'.

In the simplest case, and there may be many more elaborate cases, they found that the energy wouldn't be released unless some chemical transformations took place. If the chemical transformations took place then the energy was released, a lot of it is heat. If this just went on continuously, all you do is use up the energy. Release all of it and you've converted one chemical to another. Big deal. To get things interesting, you have to close the cycle where the chemicals can be recycled by processes of their own, and then go through it again, releasing more energy. And once you have that, you can then develop nodes — because organic chemistry is very robust, there are reaction pathways leading everywhere, which is why it's such a mess.

One doesn't need a freak set of perhaps a hundred consecutive reactions that will be needed to make an RNA, and life becomes a probable thing that can be generated through the action of the laws of chemistry and physics, provided certain conditions are met. You must have the energy. It's good to have some container or compartment, because if your products just diffuse away from each other and get lost and cease to react with one another you'll eventually extinguish the cycle. You need a compartment, you need a source of energy, you need to couple the energy to the chemistry involved, and you need a sufficiently rich chemistry to allow for this network of pathways to establish itself. Having been given this, you can then start to get evolution.
https://jsomers.net/life.pdf




Michael Polanyi: “Life’s Irreducible Structure,” published in the journal Science in 1968:
“Suppose that the actual structure of a DNA molecule were due to the fact that the bindings of its bases were much stronger than the bindings would be for any other distribution of bases, then such a DNA molecule would have no information content. Its code-like character would be effaced by an overwhelming redundancy. […] Whatever may be the origin of a DNA configuration, it can function as a code only if its order is not due to the forces of potential energy. It must be as physically indeterminate as the sequence of words is on a printed page.”

To understand why random events are not a good explanation, we best have a look at the deepest level, on an atomic scale. Life uses just five nucleobases to make DNA and RNA. Two purines, and three pyrimidines. Purines use two rings with nine atoms, pyrimidines use just one ring with six atoms. Hydrogen bonding between purine and pyrimidine bases is fundamental to the biological functions of nucleic acids, as in the formation of the double-helix structure of DNA. This bonding depends on the selection of the right atoms in the ring structure. Pyrimidine rings consist of six atoms: 4 carbon atoms and 2 nitrogen atoms. Purines have nine atoms forming the ring: 5 carbon atoms and 4 nitrogen atoms.

Remarkably, it is the composition of these atoms that permit that the strength of the hydrogen bond that permits to join the two DNA strands and form Watson–Crick base-pairing, and well-known DNA ladder.  Neither transcription nor translation of the messages encoded in RNA and DNA would be possible if the strength of the bonds had different values. Hence, life, as we understand it today, would not have arisen.

Now, someone could say, that there could be no different composition, and physical constraints and necessity could eventually permit only this specific order and arrangement of the atoms. Now, in a recent science paper from 2019, Scientists explored how many different chemical arrangements of the atoms to make these nucleobases would be possible. Surprisingly, they found well over a million variants.   The remarkable thing is, among the incredible variety of organisms on Earth, these two molecules are essentially the only ones used in life. Why? Are these the only nucleotides that could perform the function of information storage? If not, are they perhaps the best? One might expect that molecules with smaller connected Carbon components should be easier for abiotic chemistry to explore.

According to their scientific analysis, the natural ribosides and deoxyribosides inhabit a fairly redundant ( in other words, superfluous, unnecessary, needless, and nonminimal region of this space.  This is a remarkable find and implicitly leads to design. There would be no reason why random events would generate complex, rather than simple, and minimal carbon arrangements. Nor is there physical necessity that says that the composition should be so. This is evidence that a directing intelligent agency is the most plausible explanation. The chemistry space is far too vast to select by chance the right finely-tuned functional life-bearing arrangement.

In the mentioned paper, the investigators asked if other, perhaps equally good, or even better genetic systems would be possible.  Their chemical experimentations and studies concluded that the answer is no. Many nearly as good, some equally good, and a few stronger base-pairing analog systems are known. There is no reason why these structures could or would have emerged in this functional complex configuration by random trial and error. There is a complete lack of scientific-materialistic explanations despite decades of attempts to solve the riddle.

What we can see is, that direct intervention, a creative force, the activity of an intelligent agency, a powerful creator, is capable to have the intention and implement the right arrangement of every single atom into functional structures and molecules in a repetitive manner, in the case of DNA, at least 500 thousand nucleotides to store the information to kick-start life, exclusively with four bases, to produce a storage device that uses a genetic code, to store functional, instructional, complex information, functional amino acids, and phospholipids to make membranes, and ultimately, life.  Lucky accidents, the spontaneous self-organization by unguided coincidental events, that drove atoms into self-organization in an orderly manner without external direction, chemical non-biological are incapable and unspecific to arrange atoms into the right order to produce the four classes of building blocks, used in all life forms.
https://sci-hub.ren/10.1126/science.160.3834.1308

David Denton stated:
We now know not only of the existence of a break between the living and non-living world but also that it represents the most dramatic and fundamental of all the discontinuities of nature. Between a living cell and the most highly ordered non-biological systems, such as a crystal or a snowflake, there is a chasm as vast and absolute as it is possible to conceive.

And Lynn Margulis stated: To go from a bacterium to people is less of a step than to go from a mixture of amino acids to a bacterium.

And Eugene Koonin advisory editorial board of Trends in Genetics stated:
A succession of exceedingly unlikely steps is essential for the origin of life, from the synthesis and accumulation of nucleotides to the origin of translation; through the multiplication of probabilities, these make the final outcome seem almost like a miracle. The difficulties remain formidable. For all the effort, we do not currently have coherent and plausible models for the path from simple organic molecules to the first life forms. Most damningly, the powerful mechanisms of biological evolution were not available for all the stages preceding the emergence of replicator systems. Given all these major difficulties, it appears prudent to seriously consider radical alternatives for the origin of life. "

And in fact, there are basically just two options to consider: Either life emerged by a lucky accident, spontaneously through self-organization by unguided natural events, or through the direct intervention, creative force, and activity of an intelligent designer. Evolution is not a possible explanation, because evolution depends on DNA replication. Many have claimed that physical necessity could have promoted chemical reactions, which eventually resulted in the emergence of life. The problem here however is, that the genetic sequence that specifies the arrangement of proteins can be of any order, there is no constraint by physical needs.

But RNA is also incredibly complex and sensitive, and some experts are skeptical that it could have arisen spontaneously under the harsh conditions of the prebiotic world.
https://www.quantamagazine.org/lifes-first-molecule-was-protein-not-rna-new-model-suggests-20171102/

Life before DNA: The origin and evolution of early archean cells
https://www.researchgate.net/publication/270759507_Life_before_DNA_The_origin_and_evolution_of_early_archean_cells

Signature in the Cell: Chapters 9 and 10
https://sfmatheson.blogspot.com/2010/04/signature-in-cell-chapters-9-and-10.html?fbclid=IwAR2a8Qvj7SpTB5_7mLMqisb671U7Tzk3b_UoVFUbioumc-5rAIMBwe5Cbm4

Rates of decomposition of ribose and other sugars: Implications for chemical evolution 
https://pdfs.semanticscholar.org/bfa2/d96d2adb03fa603f5cdac06dd0c922fb76da.pdf?_ga=2.14589559.1378959098.1615340959-1388763040.1615340959

The peptides would have been sticky assemblies of the amino acids that were spontaneously created in the primeval chemical soup; the short peptides would have then bound to one another, over time producing a protein capable of some sort of action. Tawfik, who is in the Institute's Biomolecular Sciences Department, says that is all well and good, "but one vital type of amino acid has been missing from that experiment and every experiment that followed in its wake: amino acids like arginine and lysine that carry a positive electric charge." These amino acids are particularly important to modern proteins, as they interact with DNA and RNA, both of which carry net negative charges. RNA is today presumed to be the original molecule that could both carry information and make copies of itself, so contact with positively-charged amino acids would theoretically be necessary for further steps in the development of living cells to occur.
https://www.sciencedaily.com/releases/2020/06/200622095023.htm




Further readings:
Biochemical fine-tuning - essential for life
https://reasonandscience.catsboard.com/t2591-biochemical-fine-tuning-essential-for-life

Chemical Etiology of Nucleic Acid Structure
http://sci-hub.ren/https://science.sciencemag.org/content/284/5423/2118

Formation of RNA Phosphodiester Bond by HistidineContaining Dipeptides
http://sci-hub.ren/https://onlinelibrary.wiley.com/doi/full/10.1002/cbic.201200643

Non-enzymatic Polymerization of Nucleic Acids from Monomers: Monomer SelfCondensation and Template-Directed Reactions
http://sci-hub.ren/https://www.eurekaselect.com/104564/article

New Twist Found in the Story of Life’s Start
https://www.quantamagazine.org/chiral-key-found-to-origin-of-life-20141126/

Chiral selection in poly(C)-directed synthesis of oligo(G)
http://sci-hub.ren/https://www.nature.com/articles/310602a0

Origins of building blocks of life: A review
https://www.sciencedirect.com/science/article/pii/S1674987117301305

Spontaneous formation and base pairing of plausible prebiotic nucleotides in water
https://www.nature.com/articles/ncomms11328

Ribose and related sugars from ultraviolet irradiation of interstellar ice analogs
http://sci-hub.ren/https://science.sciencemag.org/content/352/6282/208

Phosphodiester bond
https://en.wikipedia.org/wiki/Phosphodiester_bond

DNA & RNA: The foundation of life on Earth
http://xaktly.com/NucleicAcids.html

Life as a guide to prebiotic nucleotide synthesis
https://www.nature.com/articles/s41467-018-07220-y

The Quote Mine Project
http://www.talkorigins.org/faqs/quotes/mine/part2.html

Studies on the origin of life — the end of the beginning
http://sci-hub.ren/https://www.nature.com/articles/s41570-016-0012

The cosmological model of eternal inflation and the transition from chance to biological evolution in the history of life
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1892545/

Prebiotic Systems Chemistry: Complexity Overcoming Clutter
https://www.cell.com/chem/fulltext/S2451-9294(17)30087-6?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2451929417300876%3Fshowall%3Dtrue

Miller-Urey and Beyond: What Have We Learned About Prebiotic Organic Synthesis Reactions in the Past 60 Years?
http://sci-hub.ren/https://www.annualreviews.org/doi/abs/10.1146/annurev-earth-040610-133457

A Natural Origin-of-Life: Every Hypothetical Step Appears Thwarted by Abiogenetic Randomization
This is truly a top notch research paper on abiogenesis, where the authors deal with honesty about the problems, without sugar coat  it with evolutionary nonsense vocabulary. They go straight to the facts, expose the problems, and provide a honest conclusion.
https://osf.io/p5nw3/

Paradoxes in the origin of life
http://sci-hub.ren/https://www.ncbi.nlm.nih.gov/pubmed/25608919

Studies on the origin of life  the end of the beginning
http://sci-hub.ren/https://www.nature.com/articles/s41570-016-0012

Ring Structure for Ribose:
http://chemistry.elmhurst.edu/vchembook/543ribose.html
https://chem.libretexts.org/Bookshelves/Biological_Chemistry/Supplemental_Modules_(Biological_Chemistry)/Carbohydrates/Monosaccharides/Ribose

Ribonucleotides
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2845210/

Exploring the Emergence of RNA Nucleosides and Nucleotides on the Early Earth
https://www.mdpi.com/2075-1729/8/4/57/htm

Evolutionist criticisms of the RNA World conjecture
https://creation.com/cairns-smith-detailed-criticisms-of-the-rna-world-hypothesis

Prebiotic chemistry and the origin of the RNA world.
http://sci-hub.ren/https://www.ncbi.nlm.nih.gov/pubmed/15217990

Robert Shapiro:  A Simpler Origin for Life February 12, 2007
https://www.scientificamerican.com/article/a-simpler-origin-for-life/?fbclid=IwAR0oMG32MWATWqtqg96hC-V4MEDAQAbW6oBcg_c_FNLxAUsmX8szZja5Mo8

Linking to science papers of more recent publication, did not justify you of accusing me of lying.  You made that accusation, without considering that I might have come to my conclusion based on older scientific information, which would eventually have been overturned with more recent, and new scientific findings. That is not so. 

Selective prebiotic formation of RNA pyrimidine and DNA purine nucleosides

Selective prebiotic formation of RNA pyrimidine and DNA purine nucleosides
https://sci-hub.st/https://www.nature.com/articles/s41586-020-2330-9

Claim: In contrast to all previous attempts to synthesize purine nucleosides, our synthesis is both prebiotically plausible and strictly stereo-, regio- and furanosyl-selective for the only isomer of the deoxypurine nucleosides used in modern biology. The pathway proceeds mostly via simple hydrolysis or dry-state processes, with a key reduction step promoted by UV irradiation supported by distinct mechanisms.
Reply:  That does not solve the problem of the lack of a mechanism to select  carbon and nitrogen in the nucleobases, outlined below:

https://reasonandscience.catsboard.com/t2865-rna-dna-it-s-prebiotic-synthesis-impossible#7700

Life uses just five nucleobases to make DNA and RNA. Two purines, and three pyrimidines. Purines use two rings with nine atoms, pyrimidines use just one ring with six atoms. Hydrogen bonding between purine and pyrimidine bases is fundamental to the biological functions of nucleic acids, as in the formation of the double-helix structure of DNA. This bonding depends on the selection of the right atoms in the ring structure. Pyrimidine rings consist of six atoms: 4 carbon atoms and 2 nitrogen atoms. Purines have nine atoms forming the ring: 5 carbon atoms and 4 nitrogen atoms.

Remarkably, it is the composition of these atoms that permit that the strength of the hydrogen bond that permits to join the two DNA strands and form Watson–Crick base-pairing, and well-known DNA ladder. Neither transcription nor translation of the messages encoded in RNA and DNA would be possible if the strength of the bonds had different values. Hence, life, as we understand it today, would not have arisen.

Now, someone could say, that there could be no different composition, and physical constraints and necessity could eventually permit only this specific order and arrangement of the atoms. Now, in a recent science paper from 2019, Scientists explored how many different chemical arrangements of the atoms to make these nucleobases would be possible. Surprisingly, they found well over a million variants. The remarkable thing is, among the incredible variety of organisms on Earth, these two molecules are essentially the only ones used in life. Why? Are these the only nucleotides that could perform the function of information storage? If not, are they perhaps the best? One might expect that molecules with smaller connected Carbon components should be easier for abiotic chemistry to explore.

According to their scientific analysis, the natural ribosides and deoxyribosides inhabit a fairly redundant ( in other words, superfluous, unnecessary, needless, and nonminimal region of this space. This is a remarkable find and implicitly leads to design. There would be no reason why random events would generate complex, rather than simple, and minimal carbon arrangements. Nor is there physical necessity that says that the composition should be so. This is evidence that a directing intelligent agency is the most plausible explanation. The chemistry space is far too vast to select by chance the right finely-tuned functional life-bearing arrangement.

In the mentioned paper, the investigators asked if other, perhaps equally good, or even better genetic systems would be possible. Their chemical experimentations and studies concluded that the answer is no. Many nearly as good, some equally good, and a few stronger base-pairing analog systems are known. There is no reason why these structures could or would have emerged in this functional complex configuration by random trial and error. There is a complete lack of scientific-materialistic explanations despite decades of attempts to solve the riddle.

Claim: Evidence implies that life may have started with a heterogeneous nucleic acid genetic system that included both RNA and DNA.
Reply: Even IF a prebiotic route of DNA synthesis would be found, the transition to an enzymatic biosynthesis pathway is a huge gap. How do you go from one to the other?
The replacement of RNA as the repository of genetic information by its more stable cousin, DNA, provides a more reliable way of transmitting information. DNA uses thymine (T) as one of its four informational bases, whereas RNA uses uracil (U).  At the C2' position of ribose, an oxygen atom is removed. The remarkable enzymes that do this are named Ribonucleotide reductases (RNR).  The iron-dependent enzyme is essential for DNA synthesis, and most essential enzymes of life 32 , and it has one of the most sophisticated allosteric regulations known today. 50  
The thymine-uracil exchange constitutes one of the major chemical differences between DNA and RNA. Before being incorporated into the chromosomes, this essential modification takes place. Uracil bases in RNA are transformed into thymine bases in DNA. The synthesis of thymine requires seven enzymes. De novo biosynthesis of thymine is an intricate and energetically expensive process. 
All in all, not considering the metabolic pathways and enzymes required to make the precursors to start RNA and DNA synthesis requires at least 26  enzymes.

Open questions in prebiotic chemistry to explain the origin of the four basic building blocks of life

https://reasonandscience.catsboard.com/t1279p75-abiogenesis-is-mathematically-impossible#7759

One of the few biologists, Eugene Koonin, Senior Investigator at the National Center for Biotechnology Information, a recognized expert in the field of evolutionary and computational biology, is honest enough to recognize that abiogenesis research has failed. He wrote in his book: The Logic of Chance page 351:
" Despite many interesting results to its credit, when judged by the straightforward criterion of reaching (or even approaching) the ultimate goal, the origin of life field is a failure—we still do not have even a plausible coherent model, let alone a validated scenario, for the emergence of life on Earth. Certainly, this is due not to a lack of experimental and theoretical effort, but to the extraordinary intrinsic difficulty and complexity of the problem. A succession of exceedingly unlikely steps is essential for the origin of life, from the synthesis and accumulation of nucleotides to the origin of translation; through the multiplication of probabilities, these make the final outcome seem almost like a miracle.

Eliminative inductions argue for the truth of a proposition by demonstrating that competitors to that proposition are false. Either the origin of the basic building blocks of life and self-replicating cells are the result of the creative act by an intelligent designer, or the result of unguided random chemical reactions on the early earth. Science, rather than coming closer to demonstrate how life could have started, has not advanced and is further away to generating living cells starting with small molecules.  Therefore, most likely, cells were created by an intelligent designer.

I have listed  27 open questions in regard to the origin of RNA and DNA on the early earth, 27 unsolved problems in regard to the origin of amino acids on the early earth, 12 in regard to phospholipid synthesis, and also unsolved problems in regard to carbohydrate production. The open problems are in reality far greater. This is just a small list. It is not just an issue of things that have not yet been figured out by abiogenesis research, but deep conceptual problems, like the fact that there were no natural selection mechanisms in place on the early earth.  

The implausibility of prevital RNA and DNA  synthesis

How would prebiotic processes have purified the starting molecules to make RNA and DNA which were grossly impure? They would have been present in complex mixtures that contained a great variety of reactive molecules.
How did the Synthesis of the nitrogenic nucleobases in prebiotic environments occur?
How did fortuitous accidents select the five just-right nucleobases to make DNA and RNA, Two purines, and three pyrimidines?
How did unguided random events select purines with two rings, with nine atoms, forming the two rings: 5 carbon atoms and 4 nitrogen atoms, amongst almost unlimited possible configurations?
How did stochastic coincidence select pyrimidines with one ring, with six atoms, forming its ring: 4 carbon atoms and 2 nitrogen atoms, amongst an unfathomable number of possible configurations?
How did random trial and error foresee that this specific atomic arrangement of the nucleobases is required to get the right strength of the hydrogen bond to join the two DNA strands and form Watson–Crick base-pairing?
How did mechanisms without external direction foresee that this specific atomic arrangement would convey one of, if not the best possible genetic system to store information?
How would these functional bases have been separated from the confusing jumble of similar molecules that would also have been made?
How were high-energy precursors to produce purines and pyrimidines produced in a sufficiently concentrated form and joined to the assembly site?
How could the adenine-uracil interaction function in any specific recognition scheme under the chaotic conditions of a "prebiotic soup" considering that its interaction is weak and nonspecific?
How could sufficient uracil nucleobases accumulate in prebiotic environments in sufficient quantities, if it has a half-life of only 12 years at 100◦C ?
How could the ribose 5 carbon sugar rings which form the RNA and DNA backbone have been selected, if 6 or 4 carbon rings, or even more or less, are equally possible but non-functional?
How could the formose reaction build the sugar portion of RNA from formaldehyde, if this reaction creates a mixture of sugars with varying sizes and shapes, of which ribose makes up less than 1%?
How would the functional ribose molecules have been separated from the non-functional sugars?
How were the correct nitrogen atom of the base and the correct carbon atom of the sugar selected to be joined together?
How could right-handed configurations of RNA and DNA have been selected in a racemic pool of right and left-handed molecules? Ribose must have been in its D form to adopt functional structures ( The homochirality problem )
How could random events have brought all the 3 parts together and bonded them in the right position ( probably over one million nucleotides would have been required ?)
How could prebiotic reactions have produced functional nucleosides? (There are no known ways of bringing about this thermodynamically uphill reaction in aqueous solution)
How could prebiotic glycosidic bond formation between nucleosides and the base have occurred if they are thermodynamically unstable in water, and overall intrinsically unstable?
How could  RNA nucleotides have accumulated, if they degrade at warm temperatures in time periods ranging from nineteen days to twelve years? These are extremely short survival rates for the four RNA nucleotide building blocks.
How was phosphate, the third element, concentrated at reasonable concentrations?. (The concentrations in the oceans or lakes would have been very low)
How would prebiotic mechanisms phosphorylate the nucleosides at the correct site (the 5' position) if, in laboratory experiments, the 2' and 3' positions were also phosphorylated?
How could phosphate have been activated somehow? In order to promote the energy dispendious nucleotide polymerization reaction, and (energetically uphill) phosphorylation of the nucleoside had to be possible.
How was the energy supply accomplished to make RNA? In modern cells, energy is consumed to make RNA.
How could a transition from prebiotic to biochemical synthesis have occurred? There are a huge gap and enormous transition that would be still ahead to arrive at a fully functional interlocked and interdependent metabolic network.
How could  RNA have formed, if it requires water to make them, but RNA cannot emerge in water and cannot replicate with sufficient fidelity in water without sophisticated repair mechanisms in place?
How would the prebiotic synthesis transition of RNA to the highly regulated cellular metabolic synthesis have occurred?  The pyrimidine synthesis pathway requires six regulated steps, seven enzymes, and energy in the form of ATP.
The starting material for purine biosynthesis is Ribose 5-phosphate, a product of the highly complex pentose phosphate pathway, which uses 12 enzymes. De novo purine synthesis pathway requires ten regulated steps, eleven enzymes, and energy in the form of ATP.

DNA is more stable than RNA. uracil (U) is replaced in DNA by thymine (T)
At the C2' position of ribose, an oxygen atom is removed by hypercomplex RNR molecular machines. The thymine-uracil exchange is the major chemical difference between DNA and RNA. Before being incorporated into the chromosomes, this essential modification takes place. The synthesis of thymine requires seven enzymes. De novo biosynthesis of thymine is an intricate and energetically expensive process.
All in all, not considering the metabolic pathways and enzymes required to make the precursors to start RNA and DNA synthesis, at least 26  enzymes are required. How did these enzymes emerge, if DNA is required to make them?

So, you need 26 enzymes to make DNA. But you need enzymes to make DNA. What came first?

The synthesis of ribonucleotides RNA requires the following steps:

- synthesis of the bases
- synthesis of ribose
- bonding the bases to ribose
- bonding phosphate to the nucleosides
- activation of nucleotides
- polymerization to make oligonucleotides



Leslie E. Orgel: Self-organizing biochemical cycles  2000 Nov 7
How were ribonucleotides first formed on the primitive earth? This is a very difficult problem. Stanley Miller's synthesis of the amino acids by sparking a reducing atmosphere (2) was the paradigm for prebiotic synthesis for many years, so at first, it was natural to suppose that similar methods would meet with equal success in the nucleotide field. However, nucleotides are intrinsically more complicated than amino acids, and it is by no means obvious that they can be obtained in a few simple steps under prebiotic conditions. A remarkable synthesis of adenine (3) and more or less plausible syntheses of the pyrimidine nucleoside bases (4) have been reported, but the synthesis of ribose and the regiospecific combination of the bases, ribose, and phosphate to give β-nucleotides remain problematical.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC18793/

Robert Shapiro Do natural clays catalyze this reaction? June 2006
The attractiveness of this oligonucleotide synthesis rests in part in the ready availability of the catalyst. Montmorillonite is a layered clay mineral-rich in silicate and aluminum oxide bonds. It is widely distributed in deposits on the contemporary Earth. If the polymerization of RNA subunits was a common property of this native mineral, the case for RNA at the start of life would be greatly enhanced.
However, the “[c]atalytic activity of native montmorillonites before being converted to their homoionic forms is very poor” (Ertem 2004:567). The native clays contain bound polyvalent cations, such as Cu2, Fe3, and Zn2, that interfere with phosphorylation reactions. This handicap was overcome in the synthetic experiments by titrating the clays to a monoionic form, generally sodium, before they were used. Even after this step, the activity of the montmorillonite depended strongly on its physical source, with samples from Wyoming yielding the best results (Ferris et al. 1989; Ertem 2004). Eventually the experimenters settled on Volclay, a commercially processed Wyoming montmorillonite provided by the American Colloid Company. Further purification steps were applied to obtain the catalyst used for the “prebiotic” formation of RNA.
https://www.jstor.org/stable/10.1086/506024

David Deamer Where Did Life Begin? Testing Ideas in Prebiotic Analogue Conditions 10 February 2021 5
The polymerization results must still be classified as preliminary, however, because the exact chemical structures of the polymers formed from ribonucleotides have not been elucidated.
https://www.mdpi.com/2075-1729/11/2/134/htm

It is also certain that they are polyanions resembling RNA because they readily migrate during gel electrophoresis. Furthermore, they are recognized by the enzymes used for end labeling with P-32-ATP [url=https://reasonandscience.catsboard.com/Lipid-assisted synthesis of RNA-like polymers from mononucleotides]4[/url]
https://sci-hub.ren/10.1007/s11084-007-9113-2

Sudha Rajamani: Lipid-assisted synthesis of RNA-like polymers from mononucleotides 2008 Feb 4 : 16 November 2007
Here we show that RNA-like polymers can be synthesized non-enzymatically from mononucleotides in lipid environments.

My comment: This presupposes that there actually was a lipid environment. This is an unwarranted assumption. And polymerization also assumes that right-handed RNAs were readily concentrated and available. Another unwarranted assumption. And it assumes that RNA's had a "natural" drive or tendency to polymerize. Another unwarranted assumption.

Synthesis of phosphodiester bonds is driven by the chemical potential of fluctuating anhydrous and hydrated conditions, with heat providing activation energy during dehydration.

My comment:  Phosphate must still be activated in some way — for example as a linear or cyclic polyphosphate — so that (energetically uphill) phosphorylation of the nucleoside is possible. There is no explanation of how this could have occurred prebiotically in the paper. It is just taken as a given. To make standard nucleotides only the 5’- hydroxyl of the ribose has to be phosphorylated. There is nothing that prevents the nucleoside cyclic 2’,3’-phosphate as the major product, and even further, various dinucleotide derivatives and nucleoside polyphosphates are also formed which is an additional problem.  Furthermore, the nucleotides must now be activated (for example with polyphosphate) and a reasonably pure solution of these species created of reasonable concentration. Alternatively, a suitable coupling agent would have had to be fed into the system. There is no feasible explanation where it could have come from prebiotically.  Then, the activated nucleotides (or the nucleotides with coupling agent) have to polymerize now. Initially, this would have had to happen without a pre-existing polynucleotide template (this has proved very difficult to simulate; The BIG problem here is, the pre-existing polynucleotides if the key function of transmitting information to daughter molecules had to be achieved by abiotic means.

In the final hydration step, the RNA-like polymer is encapsulated within lipid vesicles.

My comment: How would that have occurred prebiotically? There have to be made many unwarranted assumptions. 1. A viable lipid vesicle had to be ready available 2. There had to be some reasons for this process to occur. 3. And even if that event happened, the "protocell" would soon disintegrate in its individual components, and become tar.

Each group of 4 vials contained a specific set of nucleotides, which in some samples were mixed with several kinds of amphiphilic molecules.

My comment: They started their experiments with nucleotides. These were not readily available prebiotically. The formation of such is a huge problem, most commonly not sufficiently acknowledged: Here the list:

Open questions in prebiotic chemistry to explain the origin of the four basic building blocks of life
https://reasonandscience.catsboard.com/t1279p75-abiogenesis-is-mathematically-impossible#7759

The total concentration of all mononucleotides was 10 mM in the original solutions.

My comment: There was neither a selection, nor concentration mechanism extant on the prebiotic earth.

We found that significant amounts of polymers had been synthesized with UV spectra matching those expected from the mixed nucleotides. Yields ranged from 50 to 300 mg depending on which nucleotides were present in the mixture. Lower yields were observed if AMP was present, either by itself or in mixtures (50–100 μg total) while higher yields were obtained with UMP by itself (150–300 μg).

My comment: Granted that by the method employed small strands were polymerized, the aforementioned hurdles and unbridgeable problems turn this finding meaningless in face of the end goal, which is to produce information-bearing DNA strands.



Andro C. Rios: On the Origin of the Canonical Nucleobases: An Assessment of Selection Pressures across Chemical and Early Biological Evolution 2013 June
Evidence suggests that many types of heterocycles ( nucleobases) could have been present on the early Earth.
The native bases of RNA and DNA are prominent examples of the narrow selection of organic molecules upon which life is based.

Question: How were the four nucleobases selected, if there was no evolutionary natural selection extant prior to when life began?

How did nature “decide” upon these specific heterocycles?

Question: Non-mental matter does not have the ability to make decisions.

It is therefore likely that the contemporary composition of nucleobases is a result of multiple selection pressures that operated during early chemical and biological evolution.

Question: Why is that likely? Is that not a just so, an ad-hoc assertion without evidence? a red herring? 

The persistence of the fittest heterocycles in the prebiotic environment towards, for example, hydrolytic and photochemical assaults, may have given some nucleobases a selective advantage for incorporation into the first informational polymers.

Question: It is observable, how evolutionary vocabulary is smuggled in into abiogenesis research. There was no evolutionary fitness prior when life began. 

The prebiotic formation of polymeric nucleic acids employing the native bases remains, however, a challenging problem to reconcile.

Question: There is no problem if we permit the inference of intelligent design, though.

Two such selection pressures may have been related to genetic fidelity and duplex stability. 

Question: There was no need for monomers to form DNA duplex forms.

The amino groups of the nucleobases in the native alphabet are absolutely essential to maintaining the fidelity of genetic information. Spontaneous deamination reactions are thus highly deleterious
https://onlinelibrary.wiley.com/doi/abs/10.1002/ijch.201300009



Origin of prebiotic nucleotides - a viable hypothesis?
https://reasonandscience.catsboard.com/t2964-origin-of-prebiotic-nucleotides-a-viable-hypothesis

DNA: Destroys the theory of Evolution. Unmasking the lies
https://reasonandscience.catsboard.com/t2719-dna-origin-of-life-scenarios#6124

Prevital unguided origin of the four basic building blocks of life: Impossible !!
https://reasonandscience.catsboard.com/t2894-prevital-unguided-origin-of-the-four-basic-building-blocks-of-life-impossible

RNA & DNA: It's prebiotic synthesis: Impossible !!  





James Watson at left and Francis Crick discovered the structure of the DNA (deoxyribonucleic acid) molecule in 1953.  DNA are the molecules which make up the “alphabet” which specifies biological heredity.  DNA are the molecules which store the blueprint of life, and as such, hold a central indispensable position.

The RNA polymerase machine complex transcribes the instructional information stored in DNA into RNA. RNA is built of (almost) the same four-letter alphabet as DNA. It is more fragile, and as such, it could also be an information carrier, but less adequate long term.

Who wants to find answers about how life started, needs to find compelling explanations about how RNA and DNA first emerged on earth. In all known living beings, genetic information flows from DNA to RNA to proteins


Their work on the structure of DNA was performed with some access to the X-ray crystallography of Maurice Wilkins and Rosalind Franklin at King's College London. Combining all of this work led to the deduction that DNA exists as a double helix. This information was critical for their further progress. They obtained this information as part of a report by Franklin to the Medical Research Council. 

The report was by no means secret, but it put the critical data on the parameters of the helix (base spacing, helical repeat, number of units per turn of the helix, and diameter of the helix) in the hands of two who had contributed none of those data. 

With this information, they could begin to build realistic models. The big problem was where to put the purine and pyrimidine bases. Details of the diffraction pattern indicated two strands, and indicated that the relatively massive phosphate ribose backbones must be on the outside, leaving the bases in the center of the double helix.


Crick, Watson and Wilkins shared the 1962 Nobel Prize for Physiology or Medicine, Franklin having died of cancer in 1958.


Four major classes of organic molecules are found in living cells. All forms of life have organic molecules and macromolecules that fall into these four broad categories, based on their chemical and biological properties: carbohydrates, lipids, proteins, and nucleic acids. 


Nucleotides are essential to cellular metabolism, and nucleic acids are the molecules of genetic information storage and expression.

General description of the structure of the RNA and DNA molecule


DNA is the molecule of life, which contains the blueprint, or instructions to make for example proteins that perform most life functions. 



Nucleotides are building blocks for DNA and RNA. The two classes of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA molecules store genetic information coded in the sequence of their building blocks.  

DNA can be considered as a modified form of RNA since the ribose sugar in RNA is transformed into deoxyribose in DNA at the 5 prime positions ( see the red circle in the picture above ), and the uracil base is methylated into thymidine ( More about this, later). The structural difference between these sugars is that ribonucleic acid contains a hydroxyl (-OH) group, whereas deoxyribonucleic acid contains only a hydrogen atom in the place of this hydroxyl group.


Nucleotides which contain deoxyribonucleic acid are known as deoxyribonucleotides.  Those containing ribonucleic acid are known as ribonucleotides. Thus, the sugar molecule determines whether a nucleotide forms part of a DNA molecule or a RNA molecule. 

These molecules consist of three components: a phosphate, a ribose sugar, and a nitrogenous (nitrogen-containing) ring compound that behaves as a base.  The nucleotide is the repeating structural unit of both DNA and RNA. 

The picture shows the repeating unit of nucleotides found in DNA and RNA. DNA and RNA contain deoxyribose and ribose respectively as its sugar and the bases attached. The locations of the attachment sites of the base and phosphate to the sugar molecule are important to the nucleotide’s function, and how prebiotic events supposedly came up with the right configuration is one of the unsolved riddles. 

The nitrogenous base






Nucleotide bases appear in two forms: A single-ring nitrogenous base, called a pyrimidine, and a double-ringed base, called a purine.






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.  

Scientists have failed to produce cytosine in spark-discharge experiments, nor has cytosine been recovered from meteorites or extraterrestrial sources. The deamination of cytosine and its destruction by other processes such as photochemical reactions place severe constraints on prebiotic cytosine syntheses. 

The origin of guanine bases has proven to be a particular challenge. While the other three bases of RNA  could be created by heating a simple precursor compound in the presence of certain naturally occurring catalysts, guanine had not been observed as a product of the same reactions.

Adenine synthesis requires unreasonable Hydrogen cyanide concentrations. Adenine deaminates 37°C with a half-life of 80 years. Therefore, adenine would never accumulate in any kind of "prebiotic soup." The adenine-uracil interaction is weak and nonspecific, and, therefore, would never be expected to function in any specific recognition scheme under the chaotic conditions of a "prebiotic soup."

Uracil has also a half-life of only 12 years at 100◦C. For nucleobases to accumulate in prebiotic environments, they must be synthesized at rates that exceed their decomposition.

Ribose: The Pentose 5 carbon sugar ring of RNA and DNA



DNA has the ribose sugar in RNA transformed into deoxyribose in DNA at the 2 prime positions. A base is attached to the 1 prime carbon atom, and a phosphate group is attached at the 5 prime positions. Compared with ribose, deoxyribose lacks a single oxygen atom at the 2 prime positions; the prefix deoxy- (meaning without oxygen) refers to this missing atom.



The pentose sugar is a 5-carbon monosaccharide. These form two groups: aldopentoses and ketopentoses. The pentose sugars found in nucleotides are aldopentoses. Deoxyribose and ribose are two of these sugars. A DNA strand is formed when the nitrogenous bases are joined by hydrogen bonds, and the phosphates of one group are joined to the pentose sugars of the next group with a phosphodiester bond.

Ribose is a monosaccharide containing five carbon atoms. d-ribose is present as the six different forms. The β-d-furanose form is extensively used in biological systems as a component of RNA. 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.


The reality of the formose reaction is that it descends into an inextricable mixture. The vast array of sugars produced is overwhelming and the intrinsic lack of selectivity for ribose is its undoing. Ultimately, the formose reaction produces a disastrously complex mixture of linear and branched aldo and keto-sugars in the racemic forms.

The consequences of such uncontrolled reactivity is that ribose is formed in less than 1% yield among a plethora of isomers and homologs. The instability of ribose prevents its accumulation and requires it to undergo extremely rapid onward conversion to ribonucleosides before the free sugar is lost to rapid degradation. 

There are no further alternatives: Either chance "choose" by lucky random events the five-membered ring ribofuranose backbone for DNA and RNA, or it was a choice by intelligence with specific purposes. What makes more sense?

This reaction requires a high concentration of  Formaldehyde, which, however, readily undergoes a variety of reactions in aqueous solutions. Another problem is that ribose is unstable and rapidly decomposes in water. 

Furthermore, as Stanley Miller and his colleagues recently reported, "ribose and other sugars have surprisingly short half-lives for decomposition at neutral pH, making it very unlikely that sugars were available as prebiotic reagents."


Leslie Orgel concludes: Some progress has been made in the search for an efficient and specific prebiotic synthesis of ribose and its phosphates. However, in every scenario, there are still a number of obstacles to the completion of a synthesis that yields significant amounts of sufficiently pure ribose in a form that could readily be incorporated into nucleotides.


There have been a wide variety of attempts and proposals to try to solve the riddle, but up to date, without success. The article in Science magazine from 2016 admits: Ribose is the central molecular subunit in RNA, but the prebiotic origin of ribose remains unknown.

And a recent research paper from 2018 reports: Even if some progress has been made to understand the ribose formation under prebiotic conditions, each suggested route presents obstacles, limiting ribose yield and purity necessary to form nucleotides. A selective pathway has yet to be elucidated.

The third component of a nucleotide is a phosphate group


Phosphorus is the third essential element making part of the structures of DNA and RNA. It is perfect to form a stable backbone for the DNA molecule. Phosphates can form two phosphodiester bonds with two sugars at the same time and connect two nucleotides. Phosphorus is difficult to dissolve, and that would be a problem both in an aquatic as-as well on a terrestrial environment.

Phosphoesters form the backbone of DNA molecules. A phosphodiester bond occurs when exactly two of the hydroxyl groups in phosphoric acid react with hydroxyl groups on other molecules to form two ester bonds.


Phosphodiester bonds are central to all life on Earth as they make up the backbone of the strands of nucleic acid. In DNA and RNA, the phosphodiester bond is the linkage between the 3' carbon atom of one sugar molecule and the 5' carbon atom of another, deoxyribose in DNA and ribose in RNA. Strong covalent bonds form between the phosphate group and two ribose 5-carbon rings over two ester bonds. 

On prebiotic earth, however, there would have been no way to activate phosphate somehow, in order to promote the energy dispendious reaction. 

That adds up to the fact that concentrations on earth are very low.  So far, no geochemical process that led to abiotic production of polyphosphates in high yield on the Earth has been discovered. 

The phosphate is connected to ribose which is connected to the nitrogenous base. Each of the 3 parts of nucleotides must be just right in size, form, and must fit together. The bonds must have the right forces in order to form the spiral form DNA molecule. And there would have to be enough units concentrated at the same place on prebiotic earth of the four bases in order to be able to form a self-replicating RNA molecule if the RNA world is supposed to be true.


A nucleotide is differentiated from a nucleoside by one phosphate group. Accordingly, a nucleotide can also be a nucleoside monophosphate. If more phosphates bond to the nucleotide (nucleoside monophosphate) it can become a nucleoside diphosphate (if two phosphates bond), or a nucleoside triphosphate (if three phosphates bond), such as adenosine triphosphate (ATP). 


Adenosine triphosphate, or ATP, is the energy currency in the cell, a crucial component of respiration and photosynthesis, amongst other processes.

The base, sugar, and phosphate need to be joined together correctly - involving two endothermic condensation reactions involved in joining the nucleotides, which means it has to absorb energy from its surroundings. In other words, compared with polymerization to make proteins, nucleotides are even harder to synthesize and easier to destroy; in fact, to date, there are no reports of nucleotides arising from inorganic compounds in primaeval soup experiments. 



Prebiotic RNA and DNA synthesis



What must be explained, is the origin and prebiotic making of nucleotides, that is adenine, guanine, cytosine,  uracil and thymine and the transition to enzymatic biosynthesis of these. 

The emergence in the 1980s of the RNA world as a major theory for the origin of life led to increased attention on the prebiotic synthesis of simple RNA and RNA-like molecules. RNA is a complex, polymeric structure. But its prebiotic synthesis faces many problems, of which we will give a closer look just to a few. 

1. Selecting the right components
1a. Selecting right-handed configurations of RNA and DNA
1b. Selecting the right backbone sugar
1c. Size Complementarity of the nucleotide bases to form a DNA strand and strands of the DNA molecule running in the opposite directions

2. Bringing all the parts together and joining them in the right position Attach the nucleic bases to the ribose and in a repetitive manner at the same, correct place, and the backbone being a repetitive homopolymer
2a. Glycosidic bond formation between nucleosides and the base
2b. Prebiotic phosphodiester bond formation
2c. Fine-tuning of the strength of the hydrogen base pairing forces

3. The instability, degradation, and asphalt problem Bonds that are thermodynamically unstable in water, and overall intrinsic instability. RNA’s nucleotide building blocks degrade at warm temperatures in time periods ranging from nineteen days to twelve years. These extremely short survival rates for the four RNA nucleotide building blocks suggest why life’s origin would have to be virtually instantaneous—all the necessary RNA molecules would have to be assembled before any of the nucleotide building blocks decayed.

4. The energy problem: Doing things costs energy. There has to be a ready source of energy to produce RNA. In modern cells, energy is consumed to make RNA. 

5. The minimal nucleotide quantity problem.  The prebiotic conditions would have had to be right for reactions to give perceptible yields of bases that could pair with each other.

6. The Water Paradox:  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.

7 .The transition problem from prebiotic to biochemical synthesis Even if all this in a freaky accident occurred by random events, that still says nothing about the huge gap and enormous transition that would be still ahead to arrive at a fully functional interlocked and interdependent metabolic network, where  complex biosynthesis pathways produce nucleotides in modern cells.


1. Selecting the right components

1a. Selecting right-handed configurations of RNA and DNA
Once the three components would have been synthesized prebiotically, they would have had to be separated from the confusing jumble of similar molecules nearby, and they would have had to become sufficiently concentrated in order to move to the next steps, to join them to form nucleosides, and nucleotides. 


At a chemical level, a deep bias permeates all of biology. The molecules that make up DNA and other nucleic acids such as RNA have an inherent “handedness.” These molecules can exist in two mirror-image forms, but only the right-handed version is found in living organisms. Handedness serves an essential function in living beings; many of the chemical reactions that drive our cells only work with molecules of the correct handedness.

DNA takes on this form for a variety of reasons, all of which have to do with intermolecular forces. The phosphate/ribose backbone of DNA is hydrophilic (water-loving), so it orients itself outward toward the solvent, while the relatively hydrophobic bases bury themselves inside.

Additionally, the geometry of the deoxyribose-phosphate linkage allows for just the right pitch, or distance between strands in the helix, a pitch that nicely accommodates base pairing. Lots of things come together to create the beautiful right-handed double-helix structure.

Production of a mixture of d- and l-sugars produces nucelotides that do not fit together properly, producing a very open, weak structure that cannot survive to replicate, catalyze, or synthesize other biological molecules.


In DNA the atoms C1', C3', and C4' of the sugar moiety are chiral, while in RNA the presence of an additional OH group renders also C2' of the ribose chiral


A biological system exclusively uses d-ribose, whereas abiotic experiments synthesize both right- and lefthanded-ribose in equal amounts. But the pre-biological building blocks of life didn’t exhibit such an overwhelming bias. Some were left-handed and some right. So how did right-handed RNA emerge from a mix of molecules? 

Some kind of symmetry-breaking process leading to enantioenriched biomonomers would have had to exist. But none is known. 


Gerald Joyce wrote a science paper which was published in Nature magazine, in 1984. His findings, published in Nature in 1984, suggested that in order for life to emerge, something first had to crack the symmetry between left-handed and right-handed molecules, an event biochemists call “breaking the mirror.”

Since then, scientists have largely focused their search for the origin of life’s handedness in the prebiotic worlds of physics and chemistry, not biology - but with no success. So what is the cop-out ? 


Pure chance !! Luck did the job. That is the only thinkable explanation. How could that be a satisfying answer in face of the immense odds? 


But then, the same author, Christian de Duve, Nobel prize winner in physiology or medicine, dismisses instant creation as " heuristically sterile". A sterile discovery ?? in other words, a discovery lacking evidence? 


In his following book, Genetics of Original Sin, he then extended a bit further, and exposed what he meant by "heuristically sterile". 

 
It is conceivable that the molecules were short enough for all possible sequences, or almost, to be realized (by way of their genes) and submitted to natural selection. So, this is the way de Duve thought that Intelligent Design could be dismissed. This coming from a Nobel prize winner in medicine is nothing short than shocking, to say the least. 

De Duve dismissed intelligent design and replaced it with natural selection. Without providing a shred of evidence. But based on pure guesswork and speculation.

1b. Selecting the right backbone ribose sugar


Another interesting observation is that RNA and DNA use a five-membered ribose ring structure as a backbone element. It is found that six-membered ring with backbones containing six carbons per sugar unit instead of five carbons and six-membered pyranose rings instead of five-membered furanose rings do not possess the capability of efficient informational Watson–Crick base-pairing. 

Therefore, these systems could not have acted as functional competitors of RNA of a genetic system, even though these six-carbon alternatives of RNA should have had a comparable chance of being formed under the conditions that formed RNA. The reason for their failure revealed itself in chemical model studies: six-carbon-six-membered-ring sugars are found to be too bulky to adapt to the requirements of Watson–Crick base-pairing within oligonucleotide duplexes.

In sharp contrast, an entire family of nucleic acid alternatives in which each member comprises repeating units of one of the four possible five-carbon sugars (ribose being one of them) turns out to be highly efficient informational base-pairing system.



But why and how would natural unguided events on early earth select what works? Observe the authors end note of above science paper: Optimization, not maximization, of base-pairing strength, was a determinant of RNA's selection. But why would unguided events select something, that by its own has no function? The five-membered furanose or six-membered pyranose ring would simply lay around and then disintegrate without any function whatsoever. 

The smuggling in of evolutionary jargon is evident, and so the fact that the authors do omit these relevant questions that should be asked in order to keep the naturalistic paradigm alive. But its also evident how nonsensical such inferences are. 

1c. Size Complementarity of the nucleotide bases to form a DNA strand

DNA molecules are asymmetrical, such property is essential in the processes of DNA replication and transcription. Above picture demonstrates why bases need to be paired between pyrimidines and purines. In molecular biology, complementarity describes a relationship between two structures each following the lock-and-key principle.



The formation of the double-helix spiral staircase-like structure, how did it arise? 


Complementarity is the base principle of DNA replication and transcription as it is a property shared between two DNA or RNA sequences, such that when they are aligned antiparallel to each other, the nucleotide bases at each position in the sequences will be complementary, much like looking in the mirror and seeing the reverse of things. This complementary base pairing is essential for cells to copy information from one generation to another.







There is no reason why these structures could or would have emerged in this functional complex configuration by random trial and error processes. Above paper from Nature magazine, from 2016, demonstrates the complete lack of explanations despite of decades of attempts to solve the riddle. 

2. Bringing all the parts together and joining them in the right position


  
Once all the parts would have been available, they would have had to be joined together to the same assembly site,  and sorted out from non-functional molecules.  Joining all three components together involves two difficult reactions: formation of a glycosidic bond, with the right stereochemistry linking the nucleobase and ribose, and phosphorylation of the resulting nucleoside.




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. On the prebiotic world, for what reason would the generation of a homopolymer be useful? Consider that only random unguided events could account for the generation, which seems rationally extremely unlikely, if not impossible. The chance for that alone occurring randomly is extremely remote

2a. Glycosidic bond formation between nucleosides and the base

Whatever the mode of joining base and sugar was, it had to be between the correct nitrogen atom of the base and the correct carbon atom of the sugar.

The prebiotic synthesis of simple RNA molecules would, therefore, require an inventory of ribose and the nucleobases. Assembly of these components into proto-RNA would further require a mechanism to link the ribose and nucleobase together in  the proper configuration to form polymers, 

and then to activate the combined molecule (called a nucleoside) with a pyrophosphate or some other functional component that would promote formation of a bond between the nucleoside and the growing polymer.

Nucleosides are formed by linking an organic base ( guanine, adenine, uracil or cytosine) to a sugar (here D-ribose). This reaction looks simple, but how it could have occurred by an enzyme-free prebiotic synthesis, in particular involving pyrimidine bases, is an open question. There have been many imaginative ideas and attempts for its solution, all unsuccessful.  

In most cases the nucleoside components generated in the experiments, attempting to join the bases to the Ribose backbone represent only a minor fraction of a full suite of compounds produced, so that synthesis of a nucleoside would require either that the components be further purified or that some mechanism exist to selectively bring the components together out of a complex mixture.

How would non-guided random events be able to attach the nucleic bases to the ribose and in a repetitive manner at the same, correct place?  The coupling of ribose with a base is the first step to form RNA, and even those engrossed in prebiotic research have difficulty envisioning that process, especially for purines and pyrimidines.”

The emergence and existence of catalytic polymers are fundamental. Postulates of how polymerisation could have occurred on prebiotic earth are, therefore, another essential question that has not been elucidated.



There are no known ways of bringing about this thermodynamically uphill reaction in aqueous solution: purine nucleosides have been made by dry-phase synthesis, but not even this method has been successful for condensing pyrimidine bases and ribose to give nucleosides.

Laboratory-based chemical syntheses of ribonucleotides do most, if not all, require manipulation of sugars and nucleobases with protecting group strategies to overcome the thermodynamic and kinetic pitfalls that prevent their fusion. 


In a research paper from 2010, John D. Sutherland reported: Under plausible prebiotic conditions, condensation of nucleobases with ribose to give β-ribonucleosides is fraught with difficulties. The reaction with purine nucleobases is low-yielding and the reaction with the canonical pyrimidine nucleobases does not work at all.  Fitting the new synthesis to a plausible geochemical scenario is a remaining challenge.

2b. The prebiotic phosphodiester bond formation problem


Another major problem that origin of life research faces is how to explain the transition from monomer ribonucleotides to polynucleotides. Phosphodiester bonds are central to all life on Earth as they make up the backbone of the strands of nucleic acid. 

In DNA and RNA, the phosphodiester bond is the linkage between the 3' prime carbon atom of one sugar molecule and the 5' prime carbon atom of another, deoxyribose in DNA and ribose in RNA.

In modern cells, in order for the phosphodiester bond to be formed and the nucleotides to be joined, the tri-phosphate or di-phosphate forms of the nucleotide building blocks are broken apart to give off energy required to drive the enzyme-catalyzed reaction.

Once a single phosphate or two phosphates (pyrophosphates) break apart and participate in a catalytic reaction, the phosphodiester bond is formed.

The general problem regarding the condensation of small organic molecules to form macromolecules in an aqueous environment is the thermodynamically unfavorable process of water removal. In the current biosphere, these types of reactions are catalyzed by enzymes and energetically driven by pyrophosphate hydrolysis.

Obviously, biocatalysts and energy-rich inorganic phosphorus species were not extant on the Earth before life began. In all cases, the starting problem in a prebiotic synthesis would be the fact that materials would consist of an enormous amount of disparate molecules lying around unordered, and would have had to be separated and sorted out.


The intrinsic nature of the phosphodiester bonds is also finely-tuned. For instance, the phosphodiester linkage that bridges the ribose sugar of RNA could involve the 5’ OH of one ribose molecule with either the 2’ OH or 3’ OH of the adjacent ribose molecule. RNA exclusively makes use of 5’ to 3’ bonding. There are no explanations of how the right position could have been selected abiotically in a repeated manner in order to produce functional polynucleotide chains. 

As it turns out, the 5’ to 3’ linkages impart far greater stability to the RNA molecule than does the 5’ to 2’ bonds. Nucleotides can polymerize via condensation reactions.. Ribonucleotides are shown above, but the same reaction occurs between deoxyribonucleotides.


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. On 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 polymerised. Initially, this could not have happened with a pre-existing polynucleotide template.



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. .  

 



Above science paper admits: "A fundamental requirement of the RNA world hypothesis is a plausible nonenzymatic polymerisation of ribonucleotides that could occur in the prebiotic environment, but the nature of this process is still an open issue."


In present-day cells, polymerisation is carried out by enzymes with high efficiency and specificity. Enzymes are genetically encoded polymers requiring a complex, protein-based synthetic machinery

Observe what they write at the conclusion: " Selection toward highly efficient catalytic peptides, which eventually resulted in present-day enzymes, could have started at a very early stage of chemical evolution." 


This is an entirely unsupported claim. Readers without training in biochemistry will simply believe it, without further questioning. And that is what goes in basically the entire scientific literature that deals with origins. Nothing besides just so stories based on evolutionary guesswork !!

In living organisms today, adenosine-5'-triphosphate (ATP) is used for activation of nucleoside phosphate groups, but ATP would not be available for prebiotic syntheses. Joyce and Orgel note the possible use of minerals for polymerization reactions, but then express their doubts about this possibility

2c. Fine-tuning of the strength of the hydrogen base pairing forces 


Hydrogen bond base pairing forces are essential for the mechanisms associated with DNA stability.

[size=12]DNA  has by its own no function. Its purpose is to be used as "letters", storing codified instructional complex information based on their specific sequences arranged in the DNA molecules.[/size]

[size=12]It is sufficiently striking already to know that the universe, its initial conditions, cosmic constants, physical laws, and conditions on earth must be finely tuned for the emergence and flourishing of life.  What is less known however is, that fine-tuning is also extending and required in biochemistry.[/size]

Fine-tuning in biochemistry is represented by the strength of the chemical bonds that makes the universal genetic code possible. Neither transcription nor translation of the messages encoded in RNA and DNA would be possible if the strength of the bonds had different values. Hence, life, as we understand it today, would not have arisen.

As it happens, the average bond energy of a carbon-oxygen double bond is about 30 kilocalories per mol higher than that of a carbon-carbon or carbon-nitrogen double bond, a difference that is life essential. If it were not so, Watson–Crick base-pairing would not exist – nor would the kind of life we know.


3. The instability, degradation, and asphalt problem 

The chemical instability of RNA is explained by the presence of a hydroxyl group in position 2’, which results in an easy strand cleavage through an intramolecular reaction. Such a cleavage is impossible in DNA, where the hydroxyl group at 2’ is absent.




“An enormous amount of empirical data have established, as a rule, that organic systems, given energy and left to themselves, devolve to give uselessly complex mixtures, ‘asphalts’ .” In summary, the asphalt problem, also known as the tar problem, is the typical, expected outcome of prebiotic processes. 

Randomly joined assemblies of random molecules of either covalent or hydrogen bonds should plausibly form random, chaotic mixtures not linear polymers. This has been repeatedly, consistently observed experimentally.

Furthermore, RNA typically degrades in a matter of days and there is no known mechanism to remove the products of degradation from the setting. Eventually, accumulated degradation products should present yet another layer of contamination. 

Natural processes tend to make many more wrong products than usable ones and the ratio is plausibly large enough to prove fatal to abiogenesis.

Stanley L. Miller concluded that the instability of ribose stemming from its carbonyl group “preclude[s] the use of ribose and other sugars as prebiotic reagents. . . . It follows that ribose and other sugars were not components of the first genetic material.”

4. The energy problem



Prebiotic processes are similar in character to dumping a tank of gasoline on a car and igniting it.  By contrast, living cells have machinery which converts energy appearing in a specified form into ATP, the energy currency of the cell, which is useful for biotic processes. 

The form of energy to be converted into ATP varies among cellular types, such as UV light, visible light, methane, metallic ion flow, or digestible nutrients. 


Without machinery matched to the form of energy, energy tends either to have no effect or to act as a tank of gas dumped on a car.


How an ordered energy supply got " off the hook" is a serious enigma and conundrum. It is as if a rock chose a road to roll upwards, 




or a rusty nail "figuring out" how to spontaneously rust and add layers of galvanizing zinc on itself to fight corrosion. 




Unintelligent simple chemicals can't self-organize into instructions for building solar farms (photosystem 1 and 2 in photosynthesis), hydroelectric dams (ATP synthase), propulsion (motor proteins) , self repair (p53 tumor suppressor proteins) or self-destruct (caspases) in the event that these instructions become too damaged by the way the universe USUALLY operates.


 Abiogenesis is not an issue that scientists simply need more time to figure out but a fundamental problem with materialism

5. The minimal nucleotide quantity problem 

The prebiotic conditions would have had to be right for reactions to give perceptible yields of bases that could pair with each other. Even if prebiotic events would have been able to make RNA prebiotically, not only a few nucleotides would have been required, but trillions.  A minimal cell requires a genome of at least 541,000  nucleotides. 


Proposing that unguided random chemical reaction events would have produced trillions of repetitive units of each type of nucleotides, all right sized and complementary to form a double helix structure stretches far beyond what is plausible of what chance can do. Regardless of whether the actual minimum is 100,000  or 500,000 nucleotides, this is far beyond the possible range of a prebiotic nucleic acid generating mechanism.

It would eventually be able to generate a polymer with 200 nucleotides, which however soon would fall apart. Current understanding of information can give many explanations of the difficulties of creating it. It cannot explain where it comes from. 


The prebiotic appearance of nucleotides and long polymers is more difficult than the appearance of amino acids and proteins. Hence, it should take longer than 10^100.000  years to for the appearance of a gene with 780 nucleotides able to code for a specifically required protein. Yet, a 200  ribonucleic acid degrades in a matter of days.

It is implausible that a googol of googol years would be enough time. On a practical basis this discussion is nonsense. These numbers are so extreme that the human mind cannot comprehend their significance.

What is required here is not some wild one-off freak of an event: it is not true to say ‘it only had to happen once’. Trillions of attempts would have had to occur to start the role of  RNA's both, as a catalyst and informational carrier.
Prebiotic processes inherently function as random product generators, producing non-functional random substrates.

6. The Water Paradox 
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.

7. The transition problem from prebiotic to biochemical synthesis
Even if all this in a freaky accident occurred by random events, that still says nothing about the huge gap and enormous transition that would be still ahead to arrive at a fully functional interlocked and interdependent metabolic network and information system, where complex biosynthesis pathways produce nucleotides and all basic building blocks in modern cells. 


The huge gap cannot be outlined enough, leading straight to the famous chicken & egg situation. Chicken and egg scenarios in cellular function can be discovered at will. The essential components of a minimal cell cooperate with each other, such that when all work together life appears and missing any one of them prevents its appearance.

The gap between prebiotic chemistry and biochemistry is one of the biggest problems of abiogenesis research.  Prebiotic chemistry does not resemble extant biochemistry in terms of substrates, reaction pathways, catalysts or energy coupling.


The difficult condensation reactions to form nucleotides and polymers including RNA, DNA and polypeptides are accomplished in water, using energy in the form of ATP. None of this bears any resemblance to prebiotic chemistry proposals.

The difficulty is extrapolating backwards from the supposed so-called last universal common ancestor (LUCA) to prebiotic chemistry. LUCA certainly had genes and proteins, and that level of complexity is undeniably a long way from prebiotic chemistry.


How could chemical evolution define a proper genetic structure to instruct the make of a protein so that the protein could provide a step in the production of an essential product before all of the other proteins required in the biosynthesis pathway had appeared? There is a long list of products essential to the appearance of the first cell. 


Biological systems work as factories or machines. Cells host a big number of the most various molecular machines equal to factory production lines. DNA is trascribed to RNA, which is translated into proteins. But proteins are required to make DNA and RNA. This creates an endless loop, which is only solved when we posit that all three were created at the same time. 


Pick any one of the products, and try to explain how this product could appear apart from single-step, the sudden first appearance of all enzymes and proteins required in the production-line-like metabolic process, where several proteins work in a joint venture in a holistic manner to produce all basic building blocks, essential for life?


The scenarios of prebiotic production of the basic building blocks of life are far distant from the extremely complex metabolic pathways used in even the smallest known cells, like mycoplasma genitalum. The pathway to make pyrimidines, namely cytosine and uracil which yields RNA, and the further transformation of uracil to thymine, the base used in DNA, is extremely complex.


The pathway to make purines is even more complex, as can be seen in the picture above.  The pathway consists of 11 enzymatic steps.


The transition from RNA to DNA is extremely complex, and one enzyme deserves to be mentioned in special: Ribonucleotide Reductase. which converts Ribonucleotides to Deoxyribonucleotides used in DNA. 

Ribonucleotide Reductase are essential enzymes to sustain life in all free-living cells, providing the only known de novo pathway for the biosynthesis of deoxyribonucleotides, the immediate precursors for DNA synthesis and repair.

Consider that the making of DNA and all these extremely complex enzymes had to emerge prior when life began and without evolution. 


And that brings us again to the catch-22 situation as mentioned before:


essential basically means, irreducible....


This exposure here had not dealt with the problem of information, the fact that self-replication would only have been possible after the Eigen treshold would have been reached, and the fact that the make of proteins is an irreducibly complex process, involving besides DNA and RNA many other ingredients, as listed above. 



Unguided prebiotic synthesis of RNA and DNA: an unsolved riddle!

One of the more enigmatic and difficult problems confronting the prebiotic chemistry community is identifying how the monomers of RNA, or pre-RNA, or even non-related polymeric components selectively formed and self-assembled out of the presumed random prebiotic mixtures. 


It is in this assembly into informational polymers  where significant selection processes must have occurred not only for the base composition but also for the other components of nucleic acids (or nucleic acid alternatives and precursors). 

Nucleotide metabolism is central to all biological systems, due to their essential role in genetic information and energy transfer, which in turn suggests its possible presence in the supposed last universal common ancestor (LUCA) from which all life forms originate, that is  Bacteria, Archaea and Eukaryotic cells.


A vast number of books and scientific literature exists on this subject.  For several decades, the best chemists in the world have vigorously addressed the problem of the prebiotic synthesis of RNA. Their efforts however determined and imaginative their approaches, have not been encouraging.


First of all, the origin of the RNA and DNA molecule is an origin of life problem, not evolution. Evolution depends on DNA replication, therefore, DNA must have preceded evolution. And therefore, its origin cannot be explained by evolutionary mechanisms. DNA  had to emerge together with the machinery of replication and transcription as a pre-requisite for kick-starting life. 

 The supposed abiotic synthesis of RNA and thus the abiotic assembly of its components, including nucleobases, as precursors, is, therefore, a central issue in understanding the origins of life. 


This observation is highly relevant because it outlines that the origin of ribonucleotides, the building blocks of DNA, could not have emerged prior to life started, but are a pre-requisite.

 The above paper confirms this when they write: The highly conserved ribonucleotide biosynthetic pathway very likely appeared prior to the divergence of the three major lineages.  

RNA and ribonucleotides are ubiquitous and play key catalytic, structural and regulatory roles in biological processes. It is remarkable how the authors then proceed by making several claims, and inferences which are a non-sequitur based on the evidence at hand. Also, when they claim that polyribonucleotides interacted with other compounds. 

Well, before even starting about interactions of what polyribonucleotides supposedly did, it has to be explained how they came to be, which the authors confess:

 We still do not know how the RNA World first appeared. This is a remarkable admission. But then rather than elucidating why they don't know they move forward with further assertions lacking support entirely, despite they claim otherwise. 



Above is another paper which outlines that RNA and DNA had to be fully setup when life began. The authors write: Thermally stable RNA is restricted to a narrow sequence space that is incompatible with the freedom of sequence information required for an RNA genome. Therefore, LUCA must have exhibited the extant DNA/RNA dichotomy. DNA has a half-life on geologic time scales, while catalytic mRNA has a half-life on metabolic time scales.


This paper is worth mentioning for several reasons. As usual, it starts with the unsupported claim that nucleotides of RNA appear to be products of evolution.

Then, soon after, they admit that the origin of RNA is an open question. The blatant contradiction could not be more evident. In the end, outlined in red, the authors point out that there is a vast chemical space from where the possible molecules had to be separated. 

Again, it is obvious, that there is no reason whatsoever why natural causes without foresight nor goals would start such a selection process.


The book: Biological science admits:
The production of nucleotides remains a serious challenge for the theory of chemical evolution. At this time, experiments that attempt to simulate early Earth environments have yet to synthesize complete nucleotides.


Paul Davies The Algorithmic Origins of Life
Despite the conceptual elegance of the RNA world, the hypothesis faces problems, primarily due to the immense challenge of synthesizing RNA nucleotides under plausible prebiotic conditions and the susceptibility of RNA oligomers to degradation via hydrolysis.




The inevitable conclusion of this survey of nucleotide synthesis is that there is at present no convincing, prebiotic total synthesis of any of the nucleotides.

Many individual steps that might have contributed to the formation of nucleotides on the primitive Earth have been demonstrated, but few of the reactions give high yields of products, and those that do tend to produce complex mixtures of products.



Steve Benner is the founder and president of the Westheimer Corporation, a private research organization, and a prior Harvard University professor. He is one of the world’s leading authorities on abiogenesis. This is his evaluation of what he has observed: We are now 60 years into the modern era of prebiotic chemistry. 

That era has produced tens of thousands of papers attempting to define processes by which “molecules that look like biology” might arise from “molecules that do not look like biology” …. For the most part, these papers report “success” in the sense that those papers define the term…. And yet, the problem remains unsolved

Steven Benner has been remarkably courageous by admitting openly and categorically:  The “origins problem” cannot be solved. Long periods of time do not make life inevitable. Molecules rather disintegrate based on the second law of thermodynamics. and randomization turns more complete.

Since prebiotic processes are natural randomizers and abiogenesis requires specific products, it does not appear that prebiotic processes have inherent capability to meet the requirements necessitated for successful abiogenesis. This plausibly characterizes every hypothetical step of abiogenesis and explains why none have succeeded.  

Claude Shannon showed that randomization is the fundamental behavior and entropy is simply a mathematical expression of certain of its aspects


2017, english Chemist John Sutherland formed nucleotides, amongst all of the basic building blocks—lipids for compartments, amino acids for metabolism, starting with cyanide as a common initial substrate.

 However, this ended up requiring six separate ponds with their own unique geochemical conditions and whose products then needed to be mixed together in a specific sequence.

Even this degree of complexity did not supply required products, but only precursors.  The requirement of so many unique ponds and associated chemistries in such close proximity to each other, of coure, stretches plausibility.



I think, to say that on average the 14 hurdles that it would take to make primed nucleotides would each take 10 unit operations - that at least 140 little events would have to be appropriately sequenced. Unguided, the appropriate thing happened at each point on one occasion in six. 

The odds against a successful unguided synthesis of a batch of primed nucleotide on the primitive Earth would be a huge number, represented approximately by a 1 followed by 109 zeros ( 10^109).

How did Nature start to play this game? At the very least a maintained supply of primed nucleotides would be required for any kind of organism using our kind of message tapes. A nucleotide making factory would be needed.
 
'The odds are enormous against its being coincidence. No figures could express them.'

What is Benner's solution to explain how the right-handedness of ribose was selected amongst a mixed pool of enantiomeric right and left-handed ribose? In life, only right-handed ribose is viable, and biological systems exclusively use d-ribose, whereas abiotic experiments synthesize both right- and lefthanded-ribose in equal amounts. But the pre-biological building blocks of life didn’t exhibit such an overwhelming bias. Some were left-handed and some right. So how did right-handed RNA emerge from a mix of molecules?

Some kind of symmetry-breaking process leading to enantioenriched biomonomers would have had to exist. But none is known.

You resort to Benner's YouTube videos. Shall we see what he says about this issue?

https://www.youtube.com/watch?v=v5HQB3JFIZg
We've not said a word about chirality here and that's a big problem
That's all. What else did he say about it? Nothing.

RNA and DNA use a five-membered ribose ring structure as a backbone element. It is found that six-membered ring with backbones containing six carbons per sugar unit instead of five carbons and six-membered pyranose rings instead of five-membered furanose rings do not possess the capability of efficient informational Watson–Crick base-pairing.

Therefore, these systems could not have acted as functional competitors of RNA of a genetic system, even though these six-carbon alternatives of RNA should have had a comparable chance of being formed under the conditions that formed RNA. The reason for their failure revealed itself in chemical model studies: six-carbon-six-membered-ring sugars are found to be too bulky to adapt to the requirements of Watson–Crick base-pairing within oligonucleotide duplexes.

In sharp contrast, an entire family of nucleic acid alternatives in which each member comprises repeating units of one of the four possible five-carbon sugars (ribose being one of them) turns out to be highly efficient informational base-pairing system.

Stanley L. Miller concluded that the instability of ribose stemming from its carbonyl group “preclude[s] the use of ribose and other sugars as prebiotic reagents. . . . It follows that ribose and other sugars were not components of the first genetic material.”

As Shapiro has pointed out, the formose reaction which makes ribose  will not produce sugars in the presence of nitrogenous substances. These include peptides, amino acids, and amines, a category of molecules that includes the nucleotide bases. This obviously poses difficulties. First, it creates a dilemma for scenarios that envision proteins and nucleic acids arising out of a prebiotic soup rich in amino acids. Either the prebiotic environment contained amino acids, which would have prevented sugars (and thus DNA and RNA) from forming, or the prebiotic soup contained no amino acids, making protein synthesis impossible. Of course, RNA-first advocates might try to circumvent this difficulty by proposing that proteins arose well after RNA. Yet since the RNA-world hypothesis envisions RNA molecules coming into contact with amino acids early on within the first protocellular membranes, choreographing the origin of RNA and amino acids to ensure that the two events occur separately becomes a considerable problem.

James Tour:
“The coupling of a ribose with a nucleotide is the first step [in abiogenesis], and even those engrossed in prebiotic research have difficulty envisioning that process, especially for purines and pyrimidines.”

A further problem lies in the synthesis and preservation of ribose, with the right chirality. ribose is not particularly preferred over other sugars nor is it stable. Hence, an autocatalytic cycle designed to produce large amounts of carbohydrates from formaldehyde will not preferentially make ribose nor preserve it. One then faces the question of how ribose molecules were maintained against chemical processes that tend to decompose them quickly into a nondescript assemblage of polymeric mixtures. The ribose produced must have the correct handedness or chirality; on Earth, d-sugars are exclusively involved in living processes. Production of a mixture of d- and l-sugars produces nucelotides that do not fit together properly, producing a very open, weak structure that cannot survive to replicate, catalyze, or synthesize other biological molecules. In fact, the synthesis of the RNA molecule itself is interrupted by mixing nucleotides of different chirality; only in a controlled laboratory experiment or theoretical model can such an assemblage be realized.
To create a properly functioning RNA molecule out of a batch of heterochiral l- and d-sugars is a daunting challenge. The genetic template that sustains a particular kind of chemistry and set of structures is quickly lost after just one generation.

Has Benner solved all these issues? No.
Has any other scientist solved these issues? No.
Can we conclude that these issues will not be solved? Yes. The evidence points to this direction.

Purine base synthesis, by design, or non-design?

Purines are one of the two nucleobases used to make RNA and DNA. ( The others are pyrimidines). Since RNA and DNA are life-essential, the transition from prebiotic non-enzymatic, to their enzymatic synthesis had to emerge prior to the first self-replicating cells were existing. So neither evolution nor natural selection can be resorted to, to explain its origin. 

Anthony M. Pedley: A New View into the Regulation of Purine Metabolism – The Purinosome 2018 Feb 1

The de novo purine biosynthetic pathway is a highly conserved, energy-intensive pathway. In humans, this metabolic transformation is carried out in ten steps by sequential orchestration of six enzymes. The six enzymes also rely on numerous amino acid substrates and cofactors. For each molecule of IMP generated, five molecules of ATP, two molecules each of glutamine and formate, and one molecule each of glycine, aspartate, and carbon dioxide are needed. Glutamine and aspartate are generated from intermediates of the tricarboxylic acid cycle.  Formate, a metabolite exported from mitochondria, is required for the biosynthesis of the 10-formyltetrahydrofolate cofactor, which in turn is needed for the transformylase activity of GART.

Purinosome assembly in cells is proposed as a stepwise process. The exact triggers for purinosome formation are not known. Metabolic enzymes organize within the cytosol to form a given network, densely pack with myriad proteins and metabolites, to facilitate metabolic flux. One solution is through the formation of a macromolecular complex of enzymes termed a metabolon. Enzymes in other metabolic pathways such as the tricarboxylic acid cycle and glycolysis have been found to form metabolons and well-orchestrated action of these components holds the key for efficient metabolite synthesis. The resulting microenvironment sequesters reactive intermediates to enhance their stability and avoid interferences by other cellular constituents. The rationale for compartmentalization has largely relied on kinetic arguments. Specifically, the product of the first reaction in the de novo purine biosynthetic pathway, PRA, has a very short solution half-life and may directly transfer to the subsequent enzyme, GART, through complexation of the two enzymes. Similarly, GART catalyzes non-concerted steps within the same pathway and requires the activity of FGAMS for the fourth step raising the possibility that FGAMS interacts with GART.

Question: Had this complexification of two enzymes not happened right from the beginning, would that not have resulted in an error catastrophe? Was the complexification achieved by trial and error?

Behe notes that there is a fundamental quality of any irreducibly complex system in that, "any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional.” Not only have the intermediate metabolites to go through the entire biosynthesis pathway to have a function end product. But the enzymes that operate like autonomous robots have to be all there, in the right order, none of the can be missing. How did that state of affairs emerge?

On the one side you have an intelligent agency-based system of irreducible complexity of tight integrated, information-rich functional systems which have ready on-hand energy directed for such, that routinely generate the sort of phenomenon being observed.  And on the other side imagine a golfer, who has played a golf ball through an 12-hole course. Can you imagine that the ball could also play itself around the course in his absence? Of course, we could not discard, that natural forces, like wind, tornadoes or rains, or storms could produce the same result, given enough time.  the chances against it, however, are so immense, that the suggestion implies that the non-living world had an innate desire to get through the 12-hole course.


https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5272809/

De novo purine biosynthesis




Biochem (2022): Purines and pyrimidines are required for synthesizing nucleotides and nucleic acids. These molecules can be synthesized either from scratch, de novo, or salvaged from existing bases. The de novo pathway of purine synthesis is complex, consisting of 11 steps and requiring six molecules of adenosine triphosphate (ATP) for every purine synthesized. The precursors that donate components to produce purine nucleotides include glycine, ribose 5-phosphate, glutamine, aspartate, carbon dioxide, and N10-formyltetrahydrofolate (N10-formyl-FH4) (Figure below). 46


Origin of the atoms of the purine base.
FH4, tetrahydrofolate; RP, ribose 5′-phosphate. FH4, tetrahydrofolate; RP, ribose 5′-phosphate.

Comment: Every company that manufactures things, requires in many cases a purchasing department that is exclusively involved in acquiring and importing the goods, the basic materials used in the factory. That is already a complex process, requiring many different steps where communication plays a decisive role. Not any raw material can be used, but it must be the right materials, in the right quantities, in the right form, in purity, in concentrations, in sizes, etc. Once the raw materials are inside the factory of the company, the processing procedures can begin. Often these raw materials require specific processing before they can be used in the assembly process of the end product. In our case,  six(!) different atoms have to be recruited as precursors, to begin with nucleotide base synthesis. How did the LUCA get its know-how of the right atoms to make purines?   

Graham Cairns-Smith (2003): We return to questions of fine-tuning, accuracy, and specificity. Any competent organic synthesis hinges on such things. In the laboratory, the right materials must be taken from the right bottles and mixed and treated in an appropriate sequence of operations. In the living cell, there must be teams of enzymes with specificity built into them. A protein enzyme is a particularly well-tuned device. It is made to fit beautifully the transition state of the reaction it has to catalyze. Something ( or someone?) must have performed the fine-tuning necessary to allow such sophisticated molecules as nucleotides to be cleanly and consistently made in the first place.47 

Yitzhak Tor (2013):  How did nature “decide” upon these specific heterocycles? Evidence suggests that many types of heterocycles could have been present on the early Earth. It is therefore likely that the contemporary composition of nucleobases is a result of multiple selection pressures that operated during early chemical and biological evolution. The persistence of the fittest heterocycles in the prebiotic environment towards, for example, hydrolytic and photochemical assaults, may have given some nucleobases a selective advantage for incorporation into the first informational polymers.

The prebiotic formation of polymeric nucleic acids employing the native bases remains, however, a challenging problem to reconcile. Two such selection pressures may have been related to genetic fidelity and duplex stability. Considering these possible selection criteria, the native bases along with other related heterocycles seem to exhibit a certain level of fitness. We end by discussing the strength of the N-glycosidic bond as a potential fitness parameter in the early DNA world, which may have played a part in the refinement of the alphabetic bases. Even minute structural changes can have substantial consequences, impacting the intermolecular, intramolecular and macromolecular “chemical physiology” of nucleic acids 48

Biochem (2022): Purines are synthesized as ribonucleotides, with the initial purine synthesized being inosine monophosphate (IMP). Adenosine monophosphate (AMP) and guanosine monophosphate (GMP) are each derived from IMP in two-step reaction pathways. 46


D. Armenta-Medina (2014): The de novo biosynthesis of purines, starting from d-ribose-1-phosphate to inosine 5’-monophosphate (IMP) production, the main intermediate in the synthesis of ribonucleotides and deoxyribonucleotides, guanine and adenine, follows a linear branch. 

The first step is associated with phosphoglucomutase (EC 5.4.2.2) or phosphopentomutase (5.4.2.7) and 
the second step is associated with ribose-phosphate diphosphokinase (2.7.6.1); both steps are necessary for the synthesis of 5-phospho-alpha-d-ribosy-1-pyrophosphate (PRPP), which starts from d-ribose-1-phosphate. Based on their taxonomical distribution, the enzymes associated with the 5.4.2.2 and 2.7.6.1 catalytic activities were identified as being widely distributed among Bacteria, Archaea and Eukarya, suggesting the probable existence of PRPP biosynthesis in the LCA. Indeed, PRPP is a key precursor for biosynthesis in the de novo and salvage pathways for purines and pyrimidines; however, this intermediary is unstable and susceptible to hydrolysis. Therefore, it is probable that its abiotic synthesis, if it occurred, was not enough to maintain the biosynthesis in the LCA.

ANTONIO LAZCANO (1996): The purine nucleotide salvage pathways were assembled by a patchwork process that probably took place before the divergence of the three cell domains (Bacteria, Archaea, and Eucarya).43

Merriam-Webster defines patchwork as Something composed of miscellaneous or incongruous parts. It is made up of many different parts, and pieces. In other words, it is a process that relies on chance, luck, and fortunate accidents.

Comment: Could you imagine that you would yield a functional product, by putting together an assembly line, where the robots and machines to be lined up and interconnected, would be selected randomly, by a patchwork process? That is what Lazcano suggests. Any robotic production line in a factory is a highly specialized complex sophisticated system, where every part, machine, and ingredient must be carefully planned, projected, and put together in the right way, each machine lined up in the right sequence and order. Such things are not constructed by chance. Foresight is needed to know in advance what one wants to achieve. It is a process of elaborating a project first, and implementation afterward, based on the instructional blueprints coming from the engineering department. 

Geng-Min Lin (2019): Cells are the envy of chemist as they are able to build complex chemicals at high yields under ambient conditions. They excel in dictating patterns of stereochemistry and their products are impossibly functionalized. 

Stadler, R., T. Change; The Stairway To Life (2020): In all living systems, homochirality is produced and maintained by enzymes, which are themselves composed of homochiral amino acids that were specified through homochiral DNA and produced via homochiral messenger RNA, homochiral ribosomal RNA, and homochiral transfer RNA. No one has ever found a plausible abiotic explanation for how life could have become exclusively homochiral.44

Comment: The synthesis of homochiral molecules, nucleotides, amino acids, and glycerols, which are components of the heads of phospholipids, requires sophisticated enzymes, like Aspartate aminotransferases which can produce chiral amines.  

Andrzej Łyskowski (2014):ω-Transaminases are able to directly synthesize enantiopure chiral amines by catalyzing the transfer of an amino group from a primary amino donor to a carbonyl acceptor with pyridoxal 5′-phosphate (PLP) as a cofactor. In nature, (S)-selective (left) amine transaminases are more abundant than the (R)-selective (right) enzymes 45

Geng-Min Lin continues: With a view of the complex chemicals built by the natural world, it is clear that it would be revolutionary to be able to harness these processes to build unnatural molecules of such complexity by design. Their high specificity makes it more difficult to mix-and-match them between pathways as part of retrosynthetic effort.

Comment: That means, a random assembly by a patchwork process suggested by Lazcano and coworkers should be a plausible process that supposedly originated these complex biosynthesis pathways, despite the fact, that intelligent chemists have been unable to do the same!! That's a patchwork by chance of the gaps. Chance did it. The proposition is fraught with considerable problems. That takes a lot of faith since we've never observed chance or patchwork assembling a functional assembly line. Saying that something self-organizes and does it by chance is self-refuting. This is a giant leap of faith. It appears that those who point to chance, are simply putting a different name on their god (of the gaps). They make observations of the occurrence but cannot tell us how it occurred. If they think that one day in the future this will be revealed to them, and it will be a random process, they are simply exercising faith. They are also exercising the logical fallacy of Appealing to the Future. No, what one thinks might happen in the future is not proof or even evidence for your present notions. Order, information, and complexity never arise spontaneously. but are simply always the product of a conscious intelligent agent. 

Natural selection can only select an allele variation that happened by chance. We get rid of the intelligent designer, of the creator,  and then we are left, in the end, with chance. In its etymology, the word chance means mathematical probability. What is meant, however, when used related to biology, are the odds for an unpredictable event to happen. Let's suppose that the problem is just adding one enzyme to an extant metabolic pathway. That's as if I take any random robotic machine and add it to an extant assembly line. Do you get how irrational that is. Obviously, one needs to know precisely what manufacturing step that machine has to perform, what substrate it has to process, what exactly it has to do, how to hand it over to the next machine, etc.  This sounds so ridiculous and yet this is the alternative to design. It is completely incoherent and irrational.  It is logical to infer design when you see a complex assembly line, integrated and working in a factory. Claiming: "No, no, evolution made it." is rational suicide, that's incoherent and irrational. Logic abandoned leaves one with urban myths. The opposite of mythology is empirical scientific data, observable facts, and logical, plausible inferences. So in order to stay with the evolutionary narrative, one needs to reject inferences that are based on background data and experience, and stick to wishful thinking.  

Armenta-Medina continues:  Therefore, the first step for purine biosynthesis, the catalysis to ribose-5-phosphate starting from ribose 1-phosphate, is achieved by either of the two enzymes related to the enzymes EC 5.4.2.2 and 5.4.2.7. These two enzymes are analogous, since no homology at the sequence or structural level was detected. The enzyme 5.4.2.7 is partially distributed in Bacteria, mainly in free-living organisms associated with a host, such as Streptococcus pneumoniae and Lactobacillus rhamnosus; however, it was not found in archaeal and eukaryal organisms, suggesting that its emergence was posterior to the LCA divergence, probably as a secondary adaptation associated with the bacterial host. (Comment: Or the creator made them different from the get-go). 

Starting from the intermediary PRPP, in the linear branch towards IMP biosynthesis, we identified enzymes belonging to five catalytic steps (amidophosphoribosyltransferase, 2.4.2.14; phosphoribosylamine-glycine ligase, 6.3.4.13; phosphoribosylglycinamide formyltransferase, 2.1.2.2; phosphoribosylformylglycinamidine synthase, 6.3.5.3; phosphoribosylformylglycinamidine cyclo-ligase, 6.3.3.1) required for the transformation of PRPP into AIR. Most of these enzymes were identified as widely distributed in the three cellular domains, suggesting their presence in the LCA. The enzymatic step associated with EC 2.1.2.2 is responsible for the transformation of glycinamide ribotide (GAR) to formyglycinamide ribotide (FGAR) and could be carried out by two enzymes associated with different evolutionary families, PurN (Figure 1 Gold box) or phosphoribosylglycinamide formyltransferase and PurT or phosphoribosylglycinamide formyltransferase 2. Proteins associated with the PurN family use derivatives from folate synthesis as substrates. This family was identified as widely distributed in Bacteria and Eukarya and partially distributed in Archaea. Alternatively, proteins from the PurT family were partially distributed in Archaea and Bacteria and sparsely in Eukarya. It is probable that the PurT enzymatic family could have been present in the LCA, with posterior loss events in Eukarya due to its requirement for formate as a substrate. In this regard, formate is described as one-carbon donor and one of the main molecules present in prebiotics conditions, prior to folate metabolism. In a posterior phase, the emergence of folate biosynthesis might have facilitated the emergence of PurN (Figure 1, gold box), thereby achieving the co-occurrence of PurN and PurT in the LCA.


Route of de novo biosynthesis towards IMP.
In red are the enzymatic steps associated with the LCA. In green is the enzymatic synthesis towards CAIR. In pink, are the enzymatic steps specifically identified in Archaea associated with the synthesis of AICAR to IMP. In gold are the folate-dependent enzymatic steps. The asterisk shows the second catalytic activity, IMP cyclohydrolase, achieved by PurH. The precursor PRPP is also indicated.

Indeed, previous works have suggested that the emergence of PurT preceded the emergence of PurN, mainly because PurT utilizes a more primitive substrate prior to the folate-dependent pathway. One of the evolutionary pressures for the selection of PurN instead of PurT in eukaryotic organisms could be associated with the emergence of the mitochondrial respiratory chain. It has been shown that the PurT substrate, formate, is toxic and binds to cytochrome c oxidase-like, uncoupling the redox reactions and favoring the selection of PurN in eukaryotic organisms.


43. ANTONIO LAZCANO: THE ROLE OF GENE DUPLICATION IN THE EVOLUTION OF PURINE NUCLEOTIDE SALVAGE PATHWAYS 5 November, 1996
44. Change Laura Tan, Rob Stadler: The Stairway To Life: An Origin-Of-Life Reality Check  March 13, 2020 
45. Andrzej Łyskowski: Crystal Structure of an (R)-Selective ω-Transaminase from Aspergillus terreus 2014 Jan 30
46. Biochem: Purine and Pyrimidine Metabolism Aug 7, 2022
47. Graham Cairns-Smith: Fine-tuning in living systems: early evolution and the unity of biochemistry   11 November 2003
48. Yitzhak Tor: On the Origin of the Canonical Nucleobases: An Assessment of Selection Pressures across Chemical and Early Biological Evolution 2013 Jun; 5

Os pesquisadores da Universidade de Tóquio explicaram a origem da vida?

https://evolutionnews.org/2022/03/fact-check-did-university-of-tokyo-researchers-explain-the-origin-of-life/

Os investigadores começaram com um RNA “hospedeiro” de 2125 nucleotídeos emprestado de um vírus Qb. O RNA hospedeiro codifica a sequência de aminoácidos para uma das proteínas em um complexo chamado Qb replicase. A replicase transcreve o RNA, o que significa que usa modelos de RNA para criar cadeias de RNA complementares. Os pesquisadores também pegaram emprestado todo o maquinário molecular das células modernas necessário para traduzir o RNA em proteínas. O inventário de componentes translacionais fornecidos inclui dezenas de enzimas, 46 tRNAs e ribossomos.

A equipe encapsulava esse “sistema de replicação de RNA acoplado à tradução (TcRR)” em um compartimento semelhante a uma célula composto por uma emulsão de água em óleo. Todo o sistema tinha que estar contido em um volume microscópico para garantir a interação entre a replicase traduzida e o RNA hospedeiro.

Os pesquisadores implementaram um protocolo experimental meticulosamente orquestrado para conduzir a replicação do RNA e a tradução da proteína por centenas de ciclos. A replicase transcreveu o RNA hospedeiro para criar cadeias complementares. A replicase também transcreveu as fitas complementares para criar cópias do RNA hospedeiro. O sistema de tradução usou o RNA hospedeiro para fabricar a proteína necessária para criar a replicase. A transcrição e a tradução foram realizadas inteiramente pela maquinaria molecular fornecida.

Durante cada rodada de replicação, as mutações alteraram a sequência de RNA do hospedeiro, criando múltiplas variantes. Além disso, alguns eventos de replicação excluíram regiões que codificavam as informações para a replicase. As fitas de RNA resultantes não podiam mais se traduzir em replicases, então foram rotuladas como RNAs parasitas, uma vez que não desempenhavam nenhuma função.

Ao longo do tempo, diferentes variantes do hospedeiro dominaram a população e geraram replicases que transcreveram preferencialmente variantes específicas do hospedeiro e RNAs não funcionais. Além disso, os comprimentos dos RNAs não funcionais dominantes mudaram com o aumento dos ciclos de replicação. Os investigadores mapearam as eficiências relativas entre diferentes variantes de hospedeiros que se replicam entre si e entre variantes de hospedeiros que replicam parasitas. Eles descreveram como essa “rede de replicação” mudou com o tempo.

As Implicações dos Resultados

O que a equipe de pesquisa realizou? A resposta não é nada significativo. Os investigadores forneceram o maquinário necessário para conduzir externamente a replicação. Os RNAs não se replicaram nem a si mesmos nem entre si. Também não desempenharam diretamente nenhuma função biologicamente relevante. As mutações adquiridas apenas ajustaram as replicases traduzidas para executar sua função pré-existente com velocidades diferentes em diferentes variantes de hospedeiro e RNAs não funcionais, ou desativaram as replicases. Apenas o número de RNAs variantes e a velocidade de replicação mudaram. A complexidade funcional do sistema não aumentou e nada de novo surgiu.

O experimento não tem relevância para o que poderia ter acontecido na Terra primitiva. RNAs com centenas de nucleotídeos de comprimento não poderiam ter se formado. Mesmo que o fizessem, a probabilidade de suas sequências codificarem uma replicase funcional é infinitesimal. E nenhum dos componentes necessários para a tradução de proteínas existia antes do surgimento das células autônomas.

Uma rede de RNA em evolução não poderia ter surgido mesmo que a Terra contivesse vastas quantidades de RNAs codificando replicases e numerosas cópias de todos os componentes de tradução necessários. A replicação e a tradução só poderiam ter começado se o RNA, a replicase e a maquinaria de tradução migrassem para um recipiente celular microscópico. A possibilidade de tal ocorrência fortuita está além do remoto.


Os autores do artigo técnico original exageraram suas realizações e a importância de seu trabalho. O escritor simplesmente ampliou as reivindicações exageradas e expressou o estudo no contexto da narrativa secular da criação da origem da vida.

Se o escritor compreendesse totalmente a pesquisa e priorizasse a precisão científica, o resumo seria mais parecido com o seguinte:

Os pesquisadores demonstraram ainda a implausibilidade da origem da vida através de processos não direcionados. Seu experimento reforça a conclusão de que qualquer forma de replicação molecular requer uma maquinaria altamente sofisticada que só existe em células vivas. E a origem de qualquer componente celular requer informações transmitidas externamente. O estudo também desacredita ainda mais a alegação de que a evolução darwiniana poderia ter auxiliado na origem da vida, mostrando que mutações aleatórias, na melhor das hipóteses, apenas modificam ligeiramente as funções preexistentes nas proteínas. Nada de novo surge e a complexidade nunca aumenta significativamente.

The Quantum Wizardry of Life: DNA's Ingenious Mastery of the Subatomic Realm

DNA's relationship with quantum physics through various phenomena provides evidence that suggests a level of sophistication and fine-tuning that goes beyond what one might expect from purely random processes. This quantum-level sophistication in the genetic machinery of life adds another layer to the fine-tuning argument. Not only are cosmic and molecular parameters exquisitely tuned to allow for the possibility of life, but the fundamental mechanisms of life itself operate with a quantum precision that mirrors—and often surpasses—our most advanced technologies. This suggests that life isn't merely allowed by the universe's parameters; it's implemented with a level of engineering that points to an intelligence far beyond our own.

First, proton tunneling causing spontaneous mutations in DNA is a purely quantum phenomenon. Protons "tunnel" across energy barriers, leading to tautomeric shifts where hydrogen atoms end up on the wrong DNA strand, causing point mutations during replication. This process, while sometimes harmful, is also the engine of evolution, providing genetic variability for adaptation. The rate of these quantum-induced mutations seems perfectly calibrated: high enough to allow for adaptation, yet low enough to maintain genetic stability. This delicate balance suggests a system finely tuned to allow for both stability and adaptability.

Quantum entanglement plays a role in holding the DNA double helix together. The oscillations (phonons) of the nucleotide electron clouds can become entangled, preventing the helix from shaking itself apart through destructive interference. Classical physics cannot fully explain the stability of the DNA structure, yet quantum mechanics provides an elegant solution. This use of wave interference to stabilize structures is reminiscent of advanced engineering techniques we use in modern technology. That such a sophisticated technique is employed at the molecular level in every living cell is evidence of a level of design that far surpasses our current engineering capabilities.

Coherent charge transfer and electron delocalization along the DNA molecule can occur due to quantum effects. This influences gene expression by altering the molecular orbitals and electronic properties of DNA. In our most advanced electronic devices, we strive to achieve coherent charge transfer for faster, more efficient operations. The fact that DNA, the blueprint of life, employs similar quantum techniques shows it's not just a storage medium but a sophisticated computational system. The potential influence on gene expression implies a level of quantum control over biological processes, akin to the quantum control mechanisms we're just beginning to harness in cutting-edge technologies.

The chiral nature of DNA's helical structure can induce spin selectivity of charge carriers like electrons and holes. This chirality-induced spin selectivity is a quantum phenomenon that impacts DNA's chemical and physical properties. In the field of spintronics, scientists are working hard to create materials that can control electron spin, seeing it as the next frontier in computing. Yet, DNA has been doing this all along through its helical structure. This demonstrates a designed set up that anticipated concepts we're only now grasping in our most advanced research labs.

Quantum effects also play a fascinating role in the error-checking and repair mechanisms of DNA and RNA, further underscoring the sophistication of these molecular systems. These quantum phenomena contribute to the accuracy and efficiency of these critical processes, ensuring genetic stability.

1. Quantum Tunneling in DNA Repair: Just as quantum tunneling can cause mutations in DNA, it also aids in repairing them. During base excision repair (BER), glycosylase enzymes detect and remove damaged bases. Research has unraveled that these enzymes use quantum tunneling to detect mismatched protons. A proton from the enzyme tunnels along the DNA strand, sensing anomalies in the base-pairing. When it encounters a mismatch or damage, it triggers the repair process. This quantum "proofreading" method is incredibly efficient, allowing the enzyme to quickly scan long stretches of DNA without getting stuck in high-energy barriers.

The use of quantum tunneling for DNA repair is a remarkable example of foresight and deliberate design in the molecular machinery of life. Repairing things is a process that always implies an intelligent entity with goals, planning and purposeful implementation. Random, unguided processes cannot account for repair mechanisms - those require foresight to anticipate potential failures and the intentional embedding of corrective processes.

In the case of DNA repair via quantum tunneling, we see multiple layers of embedded design:

The recognition that DNA molecules are susceptible to damage and mutations that could be catastrophic if left unchecked. This awareness of potential failure points implies a thoughtful designer. The specific implementation of quantum tunneling as the mechanism to detect mismatches and trigger repairs. Tunneling is an extremely sophisticated quantum phenomenon that we struggle to fully control even in our most advanced technologies. Harnessing it for bio-molecular quality control points to a designer with mastery over quantum behavior.  The efficiency and precision built into the mechanism, allowing rapid scanning of long DNA strands without getting stuck, while pinpointing the location of errors. This is characteristic of an optimized, fault-tolerant design process.  The fact that this repair mechanism is fully integrated and present from the earliest instances of life. DNA repair is essential - if these quantum proofreading methods were not implemented from the very beginning, the first replication errors would have derailed chemical evolution before it could ever get going. The implications are inescapable - life did not start simple and accidentally acquire repair mechanisms over time. The molecular machinery underlying life shows an upfront integration of highly sophisticated, multi-layered repair processes based on cutting-edge quantum phenomena. This level of integrated complexity and foresight compellingly suggests an intelligent, purposeful design - one with an incredibly advanced understanding of quantum theory and the ability to wield it for practical applications at the bio-molecular level. Such mastery is lightyears ahead of anything we've been able to accomplish through our nascent understanding of quantum mechanics.

2. Quantum Entanglement in Mismatch Detection: Studies indicate that quantum entanglement may play a role in DNA mismatch repair. When DNA polymerase adds a new nucleotide during replication, it forms a brief quantum entanglement between the incoming nucleotide and the template base. This entanglement is sensitive to the base-pairing: a correct match maintains the entanglement, while a mismatch causes it to collapse. This quantum "quality control" mechanism allows for nearly instantaneous error detection, triggering repair processes when a mismatch is detected.

3. Coherent Energy Transfer in Nucleotide Excision Repair: In nucleotide excision repair (NER), which handles larger DNA lesions like those caused by UV radiation, quantum coherence appears to play a key role. The repair proteins use a mechanism similar to that in photosynthesis, where energy is transferred through quantum coherence. When a repair protein binds to DNA, it sets up a coherent energy transfer pathway along the DNA strand. This pathway is disrupted when it encounters a lesion, pinpointing the damage location. This quantum "damage locator" is much faster and more precise than a classical, chemical-based search.

4. Electron Delocalization in RNA Editing: RNA editing, a process that can alter the nucleotide sequence of an RNA molecule after it has been transcribed from DNA, also involves quantum effects. Some RNA editing enzymes, like Adenosine Deaminases Acting on RNA (ADARs), use electron delocalization to scan RNA molecules. The π-electrons in the RNA's nucleobases can delocalize across multiple bases, creating a quantum superposition state. This state is sensitive to base sequence and structure. When the enzyme encounters a targeted sequence, the delocalized state collapses, triggering the editing process. This quantum "sequence scanner" allows for rapid and accurate target identification.

5. Quantum Tunneling in DNA-Protein Interactions: Many DNA repair processes involve proteins recognizing specific DNA sequences or structures. Quantum tunneling facilitates this recognition. Hydrogen bonds between DNA bases and protein amino acids involve proton sharing. These protons can tunnel between the DNA and protein, creating a quantum superposition that's highly sensitive to the DNA's sequence and shape. This quantum "shape recognition" helps repair proteins quickly find their targets, like a key sensing the correct lock.

6. Spin-Selectivity in Oxidative Damage Repair: Oxidative damage to DNA often involves electron transfer processes. The chiral nature of DNA induces spin-selectivity in these electrons, a quantum effect discussed earlier. In repair processes like those involving 8-oxoguanine glycosylase (OGG1), this spin-selectivity guides the repair. Electrons with a specific spin state are more likely to be involved in the oxidative damage, and OGG1 is sensitive to this spin state. This quantum "spin filter" helps the enzyme distinguish between normal and oxidized bases, enhancing repair accuracy.

The use of quantum effects in DNA and RNA error-checking and repair mechanisms reveals an astonishing level of sophistication. These aren't just passive molecules subject to quantum effects; they're systems that actively leverage quantum mechanics for enhanced functionality. From quantum tunneling for efficient proofreading and shape recognition, to entanglement for instantaneous error detection, to coherent energy transfer for precise damage location, to electron delocalization for rapid sequence scanning, to spin-selectivity for accurate damage identification—these are techniques that we're only beginning to explore in fields like quantum computing and quantum sensing.

But the quantum sophistication doesn't stop at error-checking and repair. In the nucleus of eukaryotic cells, DNA and RNA are precisely arranged in three-dimensional space, a process also influenced by quantum effects. The packaging of DNA into chromatin involves histone proteins, around which DNA wraps. This interaction is guided by quantum phenomena. The positively charged histones and negatively charged DNA create a quantum electrodynamic field, leading to a phenomenon known as quantum electrodynamic compensation. This effect minimizes the repulsive forces between DNA segments, allowing for tighter, more precise packing.

Moreover, the folding of chromatin into higher-order structures like chromosomes involves long-range quantum entanglement. Just as entanglement stabilizes the DNA double helix, it also plays a role in maintaining these larger structures. Different regions of the DNA become quantum-mechanically entangled, creating a sort of "quantum blueprint" that guides the DNA into its correct 3D configuration. This entanglement-guided folding ensures that specific genes end up in particular nuclear regions, facilitating processes like transcription or silencing.

RNA's spatial arrangement in the nucleus is equally sophisticated. In the nucleolus, where ribosomal RNA (rRNA) is transcribed and assembled, quantum effects orchestrate a precise dance. The rRNA components use quantum coherence, similar to that in photosynthesis or DNA repair, to find their correct assembly partners. Each piece emits a unique quantum "melody," and components resonate when they've found their match, like precisely tuned quantum oscillators.

The nuclear pore complexes, which regulate the transit of RNA (and proteins) in and out of the nucleus, employ quantum tunneling and spin-selectivity. mRNA molecules, preparing to leave the nucleus, have specific "quantum barcodes" based on their nucleotide sequence. These barcodes influence the spin states and tunneling probabilities of electrons in the mRNA. The nuclear pores, sensitive to these quantum properties, allow only correctly "barcoded" mRNAs to tunnel through, ensuring only properly processed transcripts leave the nucleus.

Even epigenetic modifications, which alter gene expression without changing the DNA sequence, involve quantum mechanics. Methyl groups added to DNA in CpG islands use quantum tunneling to flip between different orientations. This quantum flipping modulates the strength of gene silencing, creating a form of "quantum epigenetic control" that fine-tunes gene expression levels. This convergence between the mechanisms in DNA/RNA and the cutting-edge of human technology is remarkable. In every field of engineering, we recognize that highly optimized, information-rich systems exhibiting such advanced techniques are the product of intelligent design. They don't arise by chance but through careful planning and execution. The fact that DNA and RNA, the blueprints and messengers of life, show these same hallmarks—at a level that often exceeds our current technological capabilities—strongly suggests that they, too, are the product of an intelligence far beyond our own. The emerging field of quantum biology isn't just revealing new mechanisms; it's unveiling a level of design in nature that points to a designer with capabilities that dwarf our most brilliant minds. The quantum phenomena in DNA and RNA—from leveraging tunneling for controlled mutation and precise packaging, to using entanglement for structural stability and 3D organization, to employing coherence for assembly and spin-selectivity for transport—all suggest systems that were intelligently designed, not randomly assembled.

When we see a computer using quantum error correction or a sensor using quantum tunneling for detection, we immediately recognize these as products of advanced engineering. They reflect not just design, but design at the forefront of human knowledge. Similarly, the quantum error-checking and repair mechanisms in DNA and RNA point to a design that's not just intelligent, but advanced beyond our current technological capabilities. This quantum-level sophistication adds another layer to the fine-tuning argument for the origin of life. The cosmic and molecular parameters that allow for life appear precisely tuned. But now we see the fundamental biological mechanisms themselves operating with a quantum precision that matches or exceeds our most sophisticated technologies. This suggests an overarching design that not only set the stage for life, but choreographed the quantum ballet that implements life at the molecular level.

The emerging field of quantum biology is revealing that quantum phenomena play a profound and pervasive role in DNA, RNA and key biological processes like replication, transcription, repair and regulation. Quantum effects like tunneling, entanglement, coherence, spin-selectivity and electron delocalization are ubiquitous, enhancing the sophistication, efficiency and accuracy of these systems. But even more significantly, these quantum phenomena are harnessed and leveraged in extremely advanced ways, employing techniques reminiscent of cutting-edge quantum technologies like quantum computing, sensing and error correction. The fact that life at the molecular level utilizes such advanced quantum capabilities strongly suggests an overarching intelligent design, crafted by a mind vastly superior to our own. Just as we infer intelligent design when we encounter sophisticated technology, the molecular quantum wizardry inherent in the machinery of life inescapably points to a superlative designer. DNA and RNA are not just subject to quantum effects, but employ them with a level of mastery that should cause us to re-evaluate our assumptions about the origin of life's dazzling sophistication.

1. Quantum Tunneling in DNA:
2. Quantum Entanglement in DNA:
3. Coherent Energy Transfer in DNA/RNA:
4. Electron Delocalization in RNA Editing:
5. Quantum Tunneling in DNA-Protein Interactions:
6. Spin-Selectivity in Oxidative Damage Repair

These papers provide experimental evidence and theoretical discussions on the various quantum phenomena observed in biological systems, particularly in DNA and RNA.

1. Quantum Tunneling and DNA Mutations:
- A theoretical analysis conducted by researchers from the University of Surrey in England revealed that quantum tunneling might play a more significant role in DNA mutations than previously thought¹.
- Specifically, they focused on the molecular bases that form the rungs of DNA's double strands. These bases are held together by hydrogen bonds, which involve protons.
- Quantum tunneling allows a proton bound to one base (cytosine) to spontaneously "tunnel" and connect with another base (guanine) on the opposite strand.
- If the proton doesn't return in time before DNA strands separate during replication, cytosine may bind to adenine instead of guanine, resulting in a mutation.
- Although these altered base pairs (called tautomers) are fleeting, the researchers found that they occur so frequently that they become a potentially rich source of mutations.
- This suggests that quantum-mechanical instability may play a crucial role in DNA mutation.

2. Implications and Design Considerations:
- The use of quantum tunneling for DNA repair indeed showcases remarkable design.
- Key design features include:
- **Awareness of Potential Failure**: The recognition that DNA is susceptible to damage and mutations implies foresight by a thoughtful designer.
- **Sophisticated Implementation**: Quantum tunneling, a complex phenomenon, serves as a precise mechanism for detecting mismatches and triggering repairs.
- **Efficiency and Precision**: The repair process efficiently scans long DNA strands without getting stuck, pinpointing error locations.
- **Early Integration**: DNA repair mechanisms were present from the earliest instances of life, suggesting upfront design.
- **Advanced Understanding**: The ability to harness quantum behavior for practical applications indicates an intelligent designer with mastery over quantum theory.

3. Further Research and Implications:
- Scientists wonder how specific repair mechanisms cope with quantum errors, given their prevalence.
- Investigating quantum-tunneling processes in DNA and cell membranes could have fundamental importance in molecular biology¹.
- Additionally, ultrafast transfer between DNA bases may play a role in common diseases¹.

For more detailed information, you can refer to the research paper published in the journal *Physical Chemistry Chemical Physics*²³. It's exciting to explore how quantum phenomena intersect with the intricate machinery of life! 🧬

(1) Quantum Tunneling Makes DNA More Unstable - Scientific American. https://www.scientificamerican.com/article/quantum-tunneling-makes-dna-more-unstable/.
(2) A new study reveals that quantum physics can cause mutations in our DNA. https://phys.org/news/2021-02-reveals-quantum-physics-mutations-dna.html.
(3) New Research Reveals That Quantum Physics Causes Mutations in Our DNA. https://scitechdaily.com/new-research-reveals-that-quantum-physics-causes-mutations-in-our-dna/.
(4) A new study reveals that quantum physics can cause mutations in our DNA .... https://www.surrey.ac.uk/news/new-study-reveals-quantum-physics-can-cause-mutations-our-dna.
(5) An open quantum systems approach to proton tunnelling in DNA - Nature. https://www.nature.com/articles/s42005-022-00881-8.pdf.


2. Quantum Entanglement in DNA
Arndt, M., Juffmann, T., & Vedral, V. (2015). Quantum Microphysics Meets Biology. Nature Communications, 6, 8520. Link. (This paper discusses the potential role of quantum entanglement in biological systems, including DNA.)

3. Coherent Energy Transfer in DNA/RNA:
Engel, G. S., Calhoun, T. R., Read, E. L., Ahn, T. K., Mančal, T., Cheng, Y. C., ... & Fleming, G. R. (2007). Evidence for Wavelike Energy Transfer Through Quantum Coherence in Photosynthetic Systems. Nature, 446(7137), 782-786. Link. (The paper provides experimental evidence for coherent energy transfer in photosynthetic systems, a phenomenon that may also play a role in DNA/RNA processes.)

4. Electron Delocalization in RNA Editing:
Sahu, S., & Ghosh, S. (2019). Quantum Delocalization in Biological Systems. International Journal of Quantum Chemistry, 119(23), e26039. Link. (This work explores the concept of quantum delocalization and its potential implications in various biological processes, including RNA editing.)

5. Quantum Tunneling in DNA-Protein Interactions:
Kosloff, R., & Masgrau, A. (2021). Quantum Tunneling in Enzyme-Catalyzed Reactions. Annual Review of Physical Chemistry, 72, 109-134. Link. (This review paper discusses the role of quantum tunneling in various enzyme-catalyzed reactions, including those involving DNA-protein interactions.)

6. Spin-Selectivity in Oxidative Damage Repair:
Zhu, Q., Kapon, Y., Fleming, A.M., Mishra, S., Santra, K., Tassinari, F., Cohen, S.R., Das, T.K., Sang, Y., Bhowmick, D.K., Burrows, C.J., Paltiel, Y., & Naaman, R. (2022). The Role of Electrons' Spin in DNA Oxidative Damage Recognition. Cell Reports Physical Science, 3(12), 101157. Link. (This experimental study demonstrates that the spin selectivity of low-energy electrons plays a crucial role in the recognition and repair of oxidative DNA damage by the enzyme OGG1 (8-oxoguanine DNA glycosylase).)

God created the most perfect quantum computer: the DNA.

In the Nature magazine article: DNA as a perfect quantum computer based on the quantum physics principles, the authors ended the article with a remarkable sentence: God created the most perfect quantum computer: the DNA. How did they come to that conclusion? The authors propose that DNA functions as a perfect quantum computer based on several key quantum physics principles and properties they believe are present in DNA. The authors argue that DNA base pairs (adenine-thymine and guanine-cytosine) can form quantum states. They propose that electrons in these base pairs create oscillatory resonant quantum states between correlated electrons and hole pairs, utilizing energy from quantized molecular vibrations.

The concept of "hole pairs" in this context is related to semiconductor physics and quantum mechanics. In semiconductors and some molecular systems, when an electron is excited from its ground state, it leaves behind a "hole" in its original energy level. A hole is essentially the absence of an electron and behaves like a positively charged particle. The authors propose that in DNA base pairs, electrons and holes form correlated pairs. This means that the movement and behavior of an electron is linked to the corresponding hole. The proposal suggests that these electron-hole pairs enter into oscillatory quantum states. These states are "resonant" because they match the frequency of molecular vibrations in the DNA. The energy for these oscillations is said to come from quantized molecular vibrations in the DNA structure. This is similar to phonons in solid-state physics, which are quantized modes of vibration in a crystal lattice. When the authors mention "hole pairs," they're referring to the correlated movement of two holes. Just as electrons can pair up in superconductors (Cooper pairs), the theory suggests that holes can also form paired states in this system. These correlated electron-hole pairs and hole-hole pairs are proposed to maintain quantum coherence, which is crucial for quantum computing.

The formation of these pairs and their quantum states is a key part of the authors' hypothesis about DNA's potential quantum computing capabilities. It's an attempt to explain how DNA might exhibit quantum behavior at a molecular level. However, this is a highly theoretical proposal. The concept of hole pairs in DNA and their role in quantum states is not a widely accepted or proven phenomenon in molecular biology or quantum physics. It represents a novel and speculative idea that would require substantial experimental evidence to verify. They suggest that the correlated electron-hole pairs in DNA behave like bosons ( Bosons are force carrier particles that mediate the fundamental forces of nature: Photons carry the electromagnetic force. Gluons carry the strong nuclear force. W and Z bosons carry the weak nuclear force ) and can form a state similar to a Bose-Einstein condensate. This quantum state is characterized by particles occupying the same quantum state, which is a key feature in quantum computing.

The authors draw parallels between the behavior of these quantum states in DNA and superconductivity. They propose that the electron-hole pairs can flow without dissipation, similar to Cooper pairs in superconductors. They argue that the hydrogen bonds between DNA base pairs act as Josephson junctions. In quantum computing, Josephson junctions are crucial components for creating superconducting qubits. The paper claims that DNA fulfills the DiVincenzo criteria, which are considered the requirements for a physical system to function as a quantum computer. These include the ability to:

- Create multiple qubits
- Initialize qubits to a known state
- Perform single and two-qubit gates
- Maintain quantum coherence
- Measure qubit states

The authors suggest that the proposed quantum states in DNA are robust against decoherence, a major challenge in quantum computing. They describe these as "topologically protected quantum memories." DNA's natural structure and replication mechanisms are seen as advantages for scalability, which is crucial for practical quantum computing. The complex, multiscale nature of DNA is viewed as an asset, potentially allowing for various levels of quantum information processing. By combining these principles and properties, the authors conclude that DNA possesses the necessary characteristics to function as a quantum computer. They view the aromatic structure of DNA bases, the hydrogen bonding between base pairs, and the overall helical structure of DNA as a naturally evolved system that exhibits quantum computing capabilities.

While the authors draw from established principles in quantum physics and known properties of DNA, their proposal represents a novel and unproven hypothesis that would require substantial experimental verification.

https://www.nature.com/articles/s41598-024-62539-5.pdf