The RNA world, and the origins of life

"The RNA World is a widely-embraced hypothetical stage of molecular evolution, devoid of protein enzymes, in which all functional catalysts were ribozymes. Only one fact concerning the RNA World can be established by direct observation: if it ever existed, it ended without leaving any unambiguous trace of itself."

https://www.sciencedirect.com/science/article/abs/pii/S0303264717302332

Even this is a bit of an understatement. Because without the prior assumption of evolution, which can and has underwritten a wide range of speculation, there is precisely zero reason to believe this wild hypothesis. No organisms have ever been discovered that demonstrate the RNA World hypothesis in action. Nor have scientists ever constructed any such organisms in their laboratories. This is not too surprising because no one has even produced anything remotely close to a detailed design of how such organisms could function.

Wills and Carter also point out negative evidences such as catalysis (RNA enzymes lack the ability to function over a wide range of temperatures) and the “impossible obstacles” to the hypothetical yet necessary transition from the RNA World to something resembling today’s extant cells. As Carter explains:

"Such a rise from RNA to cell-based life would have required an out-of-the-blue appearance of an aaRS [aminoacyl-tRNA synthetase]-like protein that worked even better than its adapted RNA counterpart. That extremely unlikely event would have needed to happen not just once but multiple times — once for every amino acid in the existing gene-protein code. It just doesn’t make sense."

https://www.sciencedaily.com/releases/2017/11/171101160756.htm

Indeed, it just doesn’t make sense. And yet in spite of these obvious problems, the RNA World has been a textbook staple, presented as a plausible and likely example of how early life evolved.

Nucleic acid instability challenges RNA world hypothesis 26 SEPTEMBER 2016
RNA and DNA have very different abilities to withstand chemical changes like depurination, deamination, and hydrolysis. The chemical stability of these two nucleic acids should also be considered when thinking about how they could become incorporated into the earliest forms of life.
https://www.chemistryworld.com/news/nucleic-acid-instability-challenges-rna-world-hypothesis/1017458.article

The stability of the RNA bases: Implications for the origin of life MATTHEW LEVY AND STANLEY L. MILLER , July 1998
High-temperature origin-of-life theories require that the components of the first genetic material are stable. We, therefore, have measured the half-lives for the decomposition of the nucleobases. They have been found to be
short on the geologic time scale. At 100°C, the growth temperatures of the hyperthermophiles, the half-lives are too short to allow for the adequate accumulation of these compounds (t1/2 for A and G ~ 1 yr; U = 12 yr; C = 19 days).
Therefore, unless the origin of life took place extremely rapidly (<100 yr), we conclude that a high-temperature origin of life may be possible, but it cannot involve adenine, uracil, guanine, or cytosine.
https://www.pnas.org/content/pnas/95/14/7933.full.pdf

PREBIOTIC RIBOSE SYNTHESIS: A CRITICAL ANALYSIS ROBERT SHAPIRO d 9 February, 1987
The evidence that is currently available does not support the availability of ribose on the prebiotic earth, except perhaps for brief periods of time, in low concentration as part of a complex mixture, and under conditions unsuitable for nucleoside synthesis.
https://sci-hub.st/https://link.springer.com/article/10.1007/BF01808782

Robert Shapiro:
The presumption that “the bases, adenine, cytosine, guanine and uracil were readily available on the early earth” is “not supported by existing knowledge of the basic chemistry of these substances. The RNA-world hypothesis faces an even more acute, but related, obstacle—a kind of catch-22. The presence of the nitrogen-rich chemicals necessary for the production of nucleotide bases prevents the production of ribose sugars. Yet both ribose and the nucleotide bases are needed to build RNA.

Dean Kenyon explains
“The chemical conditions proposed for the prebiotic synthesis of purines and pyrimidines [the bases] are sharply incompatible with those proposed for the synthesis of ribose.”

Shapiro concludes:
“The evidence that is currently available does not support the availability of ribose on the prebiotic earth, except perhaps for brief periods of time, in low concentration as part of a complex mixture, and under conditions unsuitable for nucleoside synthesis.”

Naturally occurring RNA molecules possess very few of the specific enzymatic properties of proteins. Science has shown that ribozymes can perform a few of the inumerous functions performed by proteins. Some RNA molecules can
cleave other RNA molecules (at the phosphodiester bond) (hydrolysis). Ribosomal (rRNA) performs peptide-bond formation in the peptidyl transferase center, though only in association with an additional chemical catalyst. Beyond that, RNA can perform only a few minor functional roles and then usually as the result of engineering in the laboratory. Claiming that catalytic RNA could replace proteins in the earliest stages of chemical evolution is not evidence-based.

How do you go from an RNA based world, to produce proteins? That is a huge, unsolved gap. In order to do so, you need the molecular machines that do so. The primitive replicator would need to produce RNA molecules capable of performing the functions of proteins involved in translation. These RNA molecules would need to perform the functions of the twenty specific tRNA synthetases and the fifty ribosomal proteins, among the many others involved in translation. How do you go to substitute supposed ribozymes with proteins, that later would do the same job? That's a far fetched just so scenario, which bears no evidence that such a transition could/would occur. In other words, the evolving RNA world would need to develop a coding and translation system based entirely on RNA and also generate the information necessary to build the proteins that later would be needed to replace it.

Determination of the Core of a Minimal Bacterial Gene Set
A bacterial cell depends upon a translation and coding system consisting of 106 distinct but functionally integrated proteins as well several distinct types of RNA molecules (tRNAs, mRNAs, and rRNAs) The minimal number of ribosomal proteins required for proper functioning of the ribosome corresponds to the gene set present in M. genitalium, which includes 31 proteins for the large ribosomal subunit and 19 proteins for the small one.
https://mmbr.asm.org/content/68/3/518

The prebiotic origin of nucleotides, and the RNA World

https://reasonandscience.catsboard.com/t2024p25-the-rna-world-and-the-origins-of-life#9363

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


DNA is one of the most intriguing and fascinating biomolecules found in nature. It forms the famous double helix which is elegant and beautiful. It is made of DNA (deoxyribonucleic acid) monomers, which are the molecules that make up the “alphabet” that specifies biological heredity. Life is information-driven. Specified complex information stored in genes dictates, instructs and directs the making of very complex molecular machines, autonomous robotic production lines, and chemical cell production plants, and it also directs and orders the cell to do its work, and how to operate and is as such of central importance in all life forms. Who wants to find answers about how life started, needs to find compelling explanations about how RNA and DNA first emerged on earth. The information stored in DNA is transcribed into RNA ( ribonucleic acid) and finally translated to make proteins. RNA has several other important roles in the cell. Interestingly, some viruses use RNA to store information. 

Nucleic acid research started in 1871, with a small sentence in the essay “Über die chemische Zusammensetzung der Eiterzellen” He characterized this substance as nitrogen-containing and being very rich in phosphorous. The following decades were marked by resolving the molecular structure of the “nuclein”. (“About the chemical composition of pus cells”) by Miescher 31 James Watson and Francis Crick discovered the structure of the DNA  molecule in 1953.  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. In all known living beings, genetic information flows from DNA to RNA to proteins. The work of  Watson and Crick 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.  This information was critical for their further progress. They obtained this information as part of a report by Franklin to the Medical Research Council. Combining all of this work led to the deduction that DNA exists as a double helix. 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.

RNA and DNA  are chemically unlikely molecules that are composed of three parts: a nitrogenous base, a  five-carbon sugar (pentose), and phosphate.  DNA uses thymine as a base, and RNA uses uracil. These monomers are joined to form polymers by the phosphate group. In the genome, they form double strands with Watson-Crick base-pairing. 

How did RNA synthesize prebiotically?
A number of reasons have been given why a prebiotic synthesis of RNA, and even more, DNA, is too complex. In cells, the synthesis of RNA and DNA requires extremely complex energy-demanding, finely adjusted, monitored,  and controlled anabolic pathways. Since they were not extant prebiotically, RNA had to be synthesized spontaneously on early earth by abiotic alternative non-enzymatic pathways.  This is one of the major, among many other unsolved origin of life problems. Krishnamurthy points out that "there has been some common ground on what would be needed for organic synthesis of DNA/RNA (for example, the components of ribose and nucleobases to come from formaldehyde, cyanide and their derivatives) but none of the various approaches has found universal acceptance within the origins of life community at large. 26

Over the last decades, Extraterrestrial sources like meteorites, interplanetary dust particles, hydrothermal vents in the deep ocean, and warm little ponds, a prebiotic soup, have been a few of the proposals. High-energy precursors to produce purines and pyrimidines would have had to be produced in sufficient quantities, and concentrated at a potential building site of the first cells. As we will see, there has to be put an unrealistic demand for lucky accidents, and, de facto, there is no known prebiotic route to this plausibly happening by unguided means.  

An article published in 2014 summarizes the current status quo: The first, and in some ways the most important, problem facing the RNA World is the difficulty of prebiotic synthesis of RNA. This point has been made forcefully by Shapiro and has remained a focal point of the efforts of prebiotic chemists for decades. The ‘traditional’ thinking was that if one could assemble a ribose sugar, a nucleobase, and a phosphate, then a nucleotide could arise through the creation of a glycosidic bond and a phosphodiester bond. If nucleotides were then chemically activated in some form, then they could polymerize into an RNA chain. Each of these synthetic events poses tremendous hurdles for the prebiotic Earth, not to mention the often-invoked critique of the inherent instability of RNA in an aqueous solution. Thus, the issue arises of whether there could have been a single environment in which all these steps took place. Benner has eloquently noted that single-pot reactions of sufficient complexity lead to ‘asphaltization’ (basically, the production of intractable ‘goo’). 2 

Steve Benner (2013): The late Robert Shapiro found RNA so unacceptable as a prebiotic target as to exclude it entirely from any model for the origin of life. Likewise, Stanley Miller, surveying the instability of carbohydrates in water, concluded that ‘‘neither ribose nor any other carbohydrate could possibly have been a prebiotic genetic molecule’’ (Larralde et al., 1995). Many have attempted to awaken from the RNA nightmare by proposing alternative biomolecules to replace ribose, RNA nucleobases, and/or the RNA phosphate diester linkages, another source of prebiotic difficulty. These have encountered chemical challenges of their own. 47

Steve Benner (2012): Gerald Joyce called RNA  has been called a “prebiotic chemist's nightmare” because of its combination of large size, carbohydrate building blocks, bonds that are thermodynamically unstable in water, and overall intrinsic instability. No experiments have joined together those steps ( to make RNAs) without human intervention. Further, many steps in the model have problems. Some are successful only if reactive compounds are presented in a specific order in large amounts. Failing controlled addition, the result produces complex mixtures that are inauspicious precursors for biology, a situation described as the “asphalt problem”. Many bonds in RNA are thermodynamically unstable with respect to hydrolysis in water, creating a “water problem”. Finally, some bonds in RNA appear to be “impossible” to form under any conditions considered plausible for early Earth. 48

De Duve confesses: "Unless we accept intelligent design, it is clear that the RNA precursors must have arisen spontaneously as a result of existing conditions" 21 - the problem is, - Science is clueless about how nucleotides could have been formed prebiotically.

Prof. Dr. Oliver Trapp (2019): Many questions arising from the RNA world hypothesis have not yet been answered. Among these are the transition from RNA to DNA and the pre-eminence of D-ribose in all coding polymers of life. 10

DNA and RNA: The only possible information storage molecules?
Steven A. Benner (2005): Starting in the 1980s, some synthetic biologists began to wonder whether DNA and RNA were the only molecular structures that could support genetics on Earth or elsewhere.   This knowledge, and the fact that the Watson–Crick model proposed no particular role for the phosphates in molecular recognition, encouraged the inference that the backbone could be changed without affecting pairing rules. The effort to synthesize non-ionic backbones changed the established view of nucleic acid structure. Nearly 100 linkers were synthesized to replace the 2′-deoxyribose sugar. Nearly all analogues that lacked the REPEATING CHARGE showed worse rule-based molecular recognition. Even with the most successful uncharged analogues (such as the polyamide-linked nucleic-acid analogues (PNA)) molecules longer than 15 or 20 building units generally failed to support rule-based duplex formation. In other uncharged systems, the breakdown occurs earlier. The repeating charge in the DNA backbone could no longer be viewed as a dispensable inconvenience. The same is true for the ribose backbone of RNA: The backbone is not simply scaffolding to hold the nucleobases in place; it has an important role in the molecular recognition that is central to genetics.  17

Lack of natural selection
The idea that nucleotides were readily laying around on the early earth, just waiting to be picked up, and concentrated on the building site of life, was mocked by Leslie Orgel as 'the Molecular Biologist's Dream. This is maybe the most stringent problem of prebiotic nucleotide synthesis: The materials on prebiotic earth were a mess of mixtures of lifeless chemicals, and nothing restricts the possibility of a great diversity of nucleotides with differing sugar moieties. There was no natural selection. Many science papers simply ignore this and resort nonetheless to little magic of selective pressure. It's like from Frankenstein to man. Some patchwork here and there, and chance does the rest and figures things out.  Szostak and colleagues were well aware of the problem. They wrote:

There are many nucleobase variations such as 8-oxo-purine, inosine, and the 2-thio-pyrimidines, as well as sugar variants including arabino-, 2′- deoxyribo-, and threonucleotides. The likely presence of byproducts leads to a significant problem with regard to the emergence of the RNA world, since the initially synthesized oligonucleotides would be expected to be quite heterogeneous in composition. How could such a heterogeneous mixture of oligonucleotides give rise to the relatively homogeneous RNAs that are thought to be required for the evolution of functional RNAs such as ribozymes? 30

So, in 2020, they presented a model, ignoring the fact made by Benner and others, that molecules simply disintegrate and randomize, they proposed that "  many versions of nucleotides merged to form patchwork molecules with bits of both modern RNA and DNA, as well as largely defunct genetic molecules, such as ANAThese chimeras, like the monstrous hybrid lion, eagle and serpent creatures of Greek mythology, may have been the first steps toward today's RNA and DNA." 29 Rather than focussing "on the consequences of coexisting activated arabino- and 2′-deoxy-nucleotides for nonenzymatic template-directed primer extension", the authors need to provide a plausible trajectory for how natural selection pressures provided the separation of non-canonical nucleotides to achieve a homogeneous state of affairs, where only RNA's and DNAs used in life polymerize. Often, the key questions in the mids of the often confusing technical jargon get lost.  

The nucleobases
The nucleobases are key components of RNA and DNA. The bases are divided into purines ( adenine (A) and guanine (G)) and pyrimidines [cytosine (C) and thymine (T) in DNA, and Cytosine (C) and uracil (U) in RNA]. While purines have a double ring structure and nine atoms, purines have a single ring structure with six atoms. The structural difference between these sugars is that ribonucleic acid contains a hydroxyl (-OH) group, whereas deoxyribonucleic acid contains only a hydrogen atom in place of this hydroxyl group.

Purines
Purines are one of the two compounds that are used to make the semantophoretic nucleotides RNA and DNA that store genetic information. Adenine and guanine are made of two nitrogen-containing rings. 

Adenine
One of the earliest experiments attempting to synthesize adenine in prebiotic conditions was made by Oró in 1961, where he presented evidence for the "synthesis of adenine from aqueous solutions of ammonium cyanide at temperatures below 100°." 18 In 1966, P. Ferris and L. E. Orgel pointed out, what the achilles heel was in Oró's experiment: "Adenine was formed in only 0.5% yield in Oro’s experiment; most of the cyanide formed an intractable polymer."19 Evidently, there was no prebiotic natural selection to sort out those bases that could later be used as nucleobases, from those with no function. 

Shapiro pointed out that: Useful yields of adenine cannot be obtained except in the presence of 1.0 M or stronger ammonia. The highest reasonable concentration of ammonia or ammonium ion that can be postulated in oceans and lakes on the primitive earth is about 0.01 M. Orgel  has put forward the following prerequisite for the very first information system: 'its monomeric components must have been abundant components of a prebiotic mixture of organic compounds.' Adenine does not seem to meet this requirement. The instability of adenine on a geological time scale makes its widespread prebiotic accumulation unlikely. Adenine synthesis requires unreasonable Hydrogen cyanide concentrations. Adenine plays an essential role in replication in all known living systems today and is prominent in many other aspects of biochemistry. Despite this, a consideration of its intrinsic chemical properties suggests that it did not play these roles at the very start of life. These properties include the low yields in known syntheses of adenine under authentic prebiotic conditions, its susceptibility to hydrolysis and to reaction with a variety of simple electrophiles, and its lack of specificity and strength in hydrogen bonding at the monomer and mixed oligomer level. 14

Elsewhere, Shapiro addressed an eventual extraterrestrial source: The isolation of adenine and guanine from meteorites has been cited as evidence that these substances might have been available as “raw material” on prebiotic Earth (18). However, acid hydrolyses have been needed to release these materials, and the amounts isolated have been low 5

In a recent paper from 2018, Annabelle Biscans mentions other routes investigated: Miyakama et al. suggest that purines have been formed in the atmosphere in the absence of hydrogen cyanide. They reported that guanine could have been generated from a gas mixture (nitrogen, carbon monoxide, and water) after cometary impacts. Also, it has been proposed that adenine was formed in the solar system (outside of Earth) and brought to Earth by meteorites, given the fact that adenine was found in significant quantity in carbonaceous chondrites - and concludes: Despite great efforts and impressive advancements in the study of nucleoside and nucleotide abiogenesis, further investigation is necessary to explain the gaps in our understanding of the origin of RNA. 20

Guanine
In 1984, Yuasa reported a 0.00017% yield of guanine after electrical discharge experiments. However, it is unknown if the presence of guanine was not simply resulted from a contaminant of the reaction. . S L Miller and colleagues made experiments in 1999, and yield trace amounts of guanine form by the polymerization of ammonium cyanide (0.0007% and 0.0035% depending on temperatures) indicating that guanine could arise in frozen regions of the primitive earth. 22

Abby Vogel Robinson reported in 2010: For scientists attempting to understand how the building blocks of RNA originated on Earth, guanine -- the G in the four-letter code of life -- has proven to be a particular challenge. While the other three bases of RNA -- adenine (A), cytosine (C) and uracil (U) -- 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.

Pyrimidines
Pyrimidine bases are the second of the quartet that makes up DNA that stores genetic information. Uracil ( Thymine in DNA) and cytosine are made of one nitrogen-containing ring. In 2009, Sutherland, and Szostak published a paper on a high-yielding route to activated pyrimidine nucleotides under conditions thought to be prebiotic, claiming to be "an encouraging step toward the greater goal of a plausible prebiotic pathway to RNA and the potential for an RNA world." 27 Robert Shapiro disagrees:

Although as an exercise in chemistry this represents some very elegant work, this has nothing to do with the origin of life on Earth whatsoever.  The chances that blind, undirected, inanimate chemistry would go out of its way in multiple steps and use of reagents in just the right sequence to form RNA is highly unlikely. 28

Cytosine
Scientists have failed to produce cytosine in spark-discharge experiments.

Robert Shapiro (1999): The formation of a substance in an electric spark discharge conducted in a simulated early atmosphere has also been regarded as a positive indication of its prebiotic availability. Again, low yields of adenine and guanine have been reported in such reactions, but no cytosine. The failure to isolate even traces of cytosine in these procedures signals the presence of some problem with its synthesis and/or stability. The deamination of cytosine and its destruction by other processes such as photochemical reactions place severe constraints on prebiotic cytosine syntheses.  12

Rich Deem (2001):  
Cytosine has never been found in any meteorites.
Cytosine is not produced in electric spark discharge experiments using simulated "early earth atmosphere."
Synthesis based upon cyanoacetylene requires the presence of large amounts of methane and nitrogen, however, it is unlikely that significant amounts of methane were present at the time life originated.
Synthesis based upon cyanate is problematical, since it requires concentrations in excess of 1 M (molar). When concentrations of 0.1 M (still unrealistically high) are used, no cytosine is produced.
Synthesis based upon cyanoacetaldehyde and urea suffers from the problem of deamination of the cytosine in the presence of high concentrations of urea (low concentrations produce no cytosine). In addition, cyanoacetaldehyde is reactive with a number of prebiotic chemicals, so would never attain reasonable concentrations for the reaction to occur. Even without the presence of other chemicals, cyanoacetaldehyde has a half-life of only 31 years in water.
Cytosine deaminates with an estimated half-life of 340 years, so would not be expected to accumulate over time.
Ultraviolet light on the early earth would quickly convert cytosine to its photohydrate and cyclobutane photodimers (which rapidly deaminate). 49

Uracil
In 1961, Sidney Fox and colleagues synthesized Uracil under: "thermal conditions which yield other materials of theoretical prebiochemical significance. The conditions studied in the synthesis of uracil included temperatures in the range of 100° to 140°C, heating periods of from 15 minutes to 2 hours". 33  Other attempts to provide plausible prebiotic scenarios for the non-enzymatic synthesis of nucleotides and nucleobases continue to the present day. In 2019, Okamura and colleagues published a paper on pyrimidine nucleobase synthesis where their conclusion remarks is noteworthy:

We show that the cascade reaction proceeds under one-pot conditions in a continuous manner to provide SMePy 6. Importantly the key intermediate SMePy 6 gives rise not only to canonical but also to non-canonical bases arguing for the simultaneous prebiotic formation of a diverse set of pyrimidines under prebiotically plausible conditions.

This highlights a general problem mentioned before: chemical reactions are very common resulting in a mixture of molecules, of which most are not relevant for abiogenesis. There was no mechanism to sort out those detrimental in the process towards life. 32

Fast decomposition rate
Adenine deaminates at 37°C with a half-life of 80 years (half-life = time that a substance takes to decompose, and loses half of its physiologic activity). At 100°C its half-live is 1 year. For guanine, at 100°C its half-live is 10 months, uracil is 12 years, and thymine 56 years.  For the decomposition of a nucleobase, this is very short. For nucleobases to accumulate in prebiotic environments, they must be synthesized at rates that exceed their decomposition. Therefore, adenine and the other nucleobases would never accumulate in any kind of "prebiotic soup." 14

A paper published in 2015 points out that: 

Nucleotide formation and stability are sensitive to temperature. Phosphorylation of nucleosides in the laboratory is slower at low temperatures, taking a few weeks at 65 ◦C compared with a couple of hours at 100 ◦C. The stability of nucleotides, on the other hand, is favored in warm conditions over high temperatures. If a WLP is too hot (>80 ◦C), any newly formed nucleotides within it will hydrolyze in several days to a few years. At temperatures of 5 ◦C to 35 ◦C that either characterize more-temperate latitudes or a post snowball Earth, nucleotides can survive for thousand-to-million-year timescales. However, at such temperatures, nucleotide formation would be very slow.  25

That means, in hot environments, nucleotides might form, but they decompose fast. On the other hand, in cold environments, they might not degrade that fast, but take a long time to form. Nucleotides would have to be generated by prebiotic environmental synthesis processes at a far higher rate than they are decomposed and destroyed, and accumulated and concentrated at one specific construction site. Putting that into perspective, P.Ubique, the smallest known free-living cell, has a genome size of 1,3 million nucleotides. The best-studied mechanism relevant to the prebiotic synthesis of ribose is the formose reaction. Several problems have been recognized in ribose synthesis via the formose reaction, which reaction is very complex. It depends on the presence of a suitable inorganic catalyst. Ribose is merely an intermediate product among a broad suite of compounds including sugars with more or fewer carbons. There would have been no way to activate phosphate somehow, in order to promote the energy dispendious reaction.

Extraterrestrial nucleobase sources
In april 2022, nature magazine announced the identification of nucleobases in carbonaceous meteorites.  Guanine and adenine were detected in murchison meteorite extracts, and now various pyrimidine nucleobases such as cytosine, uracil, and thymine, and their structural isomers such as isocytosine, imidazole-4-carboxylic acid, and 6-methyluracil, respectively. They came to the conclusion that "a diversity of meteoritic nucleobases could serve as building blocks of DNA and RNA on the early Earth".23 An article of NASA echoed the authors conclusion: "This discovery demonstrates that these genetic parts are available for delivery and could have contributed to the development of the instructional molecules on early Earth."24 The fatal blow is the fact that the nucleobases relevant for life come always mixed together with isomers that are irrelevant. There was no prebiotic selection to sort out and concentrate exclusively those relevant for life. 

Selecting the right backbone sugar

The difficulty to get ribose prebiotically
One of the most debated questions concerns the availability and synthesis of prebiotic ribose. 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.  Ribose is a monosaccharide containing five carbon atoms. d-ribose is present in the six different forms. 

The formose reaction
Jim Cleaves II (2011): The formose reaction, discovered by Butlerow in 1861, is a complex autocatalytic set of condensation reactions of formaldehyde to yield sugars and other small sugar-like molecules. 46
Gaspar Banfalvi (2020): Among the best-known nonenzymatic pathways to ribose formation, we find the formose (from formaldehyde and aldose words) or Butlerow reaction 44 Gerald F Joyce (2012)The classical prebiotic synthesis of sugars is by the polymerization of formaldehyde (the “formose” reaction). It yields a very complex mixture of products including only a small proportion of ribose. This reaction does not provide a reasonable route to the ribonucleotides. A number of other studies have addressed the problems presented by the lack of specificity of the formose reaction and by the instability of ribose. 43

S.Islam (2017): Several problems have been recognized for 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 are 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. 36

Irina V Delidovich and colleagues (2014): The classical formose reaction (FR) is hardly applicable for any practical purposes outside of the history of chemical science. The typical “sugary substance” formed as a result of the catalytic oligomerization of formaldehyde nowadays known as “formose” comprises dozens of straight-chain and branched monosaccharides, polyols, and polyhydroxycarbonic acids.5 

There are no further alternatives: Either chance "choose" by fortuitous random events the five-membered ring ribofuranose backbone for DNA and RNA, or it was a choice by intelligence with specific purposes. What is more plausible and probable?  The formose 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 even at low temperature and neutral pH, and as well in water. Furthermore, as Stanley Miller and his colleagues 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. 4

Leslie Orgel (2004): We conclude that 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. 34

Cairns-Smith (1990) Sugars are particularly trying. While it is true that they form from formaldehyde solutions, these solutions have to be far more concentrated than would have been likely in primordial oceans. And the reaction is quite spoilt in practice by just about every possible sugar being made at the same time - and much else besides. Furthermore the conditions that form sugars also go on to destroy them. Sugars quickly make their own special kind of tar - caramel - and they make still more complicated mixtures if amino acids are around. 1990

There have been a wide variety of attempts and proposals to try to solve the riddle, but up to date, without success. Science magazine (2016): Ribose is the central molecular subunit in RNA, but the prebiotic origin of ribose remains unknown. 35 Annabelle Biscans (2018): Even if some progress has been made to understand 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. 6

RNA and DNA use a five-membered ribose ring structure as backbone. Rings containing six carbons instead of five carbons do not possess the capability of efficient informational Watson–Crick base-pairing. Therefore, these systems could not have acted as functional competitors of RNA in 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 is the fact that six-carbon-six-membered-ring sugars are 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 a highly efficient informational base-pairing system. But why and how would natural non-designed events on early earth select what works? Observe Albert Eschenmoser's end note in his science paper from 1986: Optimization, not maximization, of base-pairing strength, was a determinant of RNA's selection. [url=https://www.science.org/doi/10.1126/science.284.5423.2118#:~:text=Chemical etiology (2) of nucleic,the molecular basis of life's]8[/url] But how and why would unintended events select something, that on its own has no function? These ring structures would simply lay around and then soon disintegrate. The smuggling in of evolutionary jargon is widespread for sake of the lack of any alternative. The authors omit and do not ask these relevant questions. That permits keeping the naturalistic paradigm alive. But it should be evident how nonsensical evolutionary claims and such inferences are. 

Ribose - the best alternative 
Prof. Gaspar Banfalvi (2006): Ribose was not randomly selected but the only choice, since β-D-ribose fits best into the structure of physiological forms of nucleic acids. 16

Ribose sugar is the molecule of choice for nucleic acids, yet because it is difficult to imagine forming under plausible prebiotic conditions and has a short lifetime, origin-of-life researchers have searched diligently for alternatives, like glycerol, that might have served as scaffolding for prebiotic chemicals prior to the emergence of DNA.  Unfortunately, they don’t work.  Steven Benner: Over 280 alternative molecules have been tested, and they just do not work at all; those that might be better than ribose are implausible under prebiotic conditions.  “Ribose is actually quite good – uniquely good,” he said.  Deal with it: one’s chemical evolution model is going to have to include ribose.  That means figuring out how it can form, how it can avoid destruction in water, and how it can avoid clumping into useless globs of tar.  (RNA, the main player in the leading “RNA World” scenario for the origin of life, uses ribose; DNA uses a closely-related sugar, deoxyribose.) 38

Various possible ribose configurations: 


Ribose can exist in various forms: α-D-ribose, β-D-ribose  ( right-handed chiral form, dextrorotary) or α-L-ribose, β-L-ribose ( left-handed chiral form, levorotary).  it can form α-nucleosides, β-nucleoside, envelope or twisted conformations,


Ribose conformations and configurations. (a) Major conformers of cyclopentane. (b) Envelope and twisted conformers of tetrahydrofuran. (c) D-configuration as well as α and β anomeric configurations of D-ribose. (d) Twisted conformations in ribose, C3′-endo in A-DNA and C2′-endo conformations in B-DNA. 44

Selecting β-nucleosides
Life uses mostly β-nucleosides rather than α-nucleosides ( which are extremely rare in biological systems). In β-nucleosides, the ribose or deoxyribose is linked to nucleobases through β-glycosidic bonds, which means that the nucleobase at C1 is cis with respect to the hydroxymethyl group at C4, known as the β-configuration. In  α-nucleosides, the nucleobase and hydroxymethyl group in the ribose or deoxyribose are in a trans relationship



Configuration of β-nucleosides and α-nucleosides

Life uses exclusively right-handed homochiral β-D-ribonucleotides. Roger D. Blandford (2020): The homochirality of the sugars has important consequences for the stability of the helix and, hence, on the fidelity or error control of the genetic code.  45

Prof. Gaspar Banfalvi (2006): Bases in α-anomeric position are unable to base-pair, eliminating the possibility of helix formation. 16

Tan, Change; Stadler, Rob. The Stairway To Life:
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. 50

Emily Singer (2016): 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. 42

Abiogenesis researchers are in the dark when it comes to explaining how the molecules of life, amongst them, the life-essential RNAs and DNAs could have been selected without a mental agency. 

Wikipedia: Like most sugars, ribose exists as a mixture of cyclic forms in equilibrium with its linear form, and these readily interconvert especially in aqueous solution.^[8] The name "ribose" is used in biochemistry and biology to refer to all of these forms, though more specific names for each are used when required. In its linear form, ribose can be recognised as the pentose sugar with all of its hydroxyl functional groups on the same side in its Fischer projection. d-Ribose has these hydroxyl groups on the right hand side and is associated with the systematic name (2R,3R,4R)-2,3,4,5-tetrahydroxypentanal,^[9] whilst l-ribose has its hydroxyl groups appear on the left hand side in a Fischer projection. Cyclisation of ribose occurs via hemiacetal formation due to attack on the aldehyde by the C4' hydroxyl group to produce a furanose form or by the C5' hydroxyl group to produce a pyranose form. In each case, there are two possible geometric outcomes, named as α- and β- and known as anomers, depending on the stereochemistry at the hemiacetal carbon atom (the "anomeric carbon"). 

Phosphorus
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. 

Libretexts explains: 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. Kitadai (2017): So far, no geochemical process that led to abiotic production of polyphosphates in high yield on the Earth has been discovered. 39 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 the 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. The Albert team explains: 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). 40 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 primeval soup experiments.

Why phosphorus?
The selection of phosphorus as a backbone of RNA and DNA was a very smart choice. F H Westheimer (1987): The existence of a genetic material such as DNA requires a compound for a connecting link that is at least divalent. In order that the resulting material remain within a membrane, it should always be charged, and therefore the linking unit should have a third, ionizable group. The linkage is conveniently made by ester bonds, but, in order that the ester be hydrolytically stable, that charge should be negative and should be physically close to the ester groups. All of these conditions are met by phosphoric acid, and no alternative is obvious. Furthermore, phosphoric acid can form monoesters of organic compounds that can decompose by a mechanism other than normal nucleophilic attack, a mechanism that allows them sufficient reactivity to function in intermediary metabolism. 15

Bonding ribose to the nucleobase, to get nucleosides
Supposing that the parts were available, they would have had to be joined together at 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. Nucleosides lack a phosphate at the C5′ position. There are no known ways of bringing about this thermodynamically uphill reaction in an 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.

John D. Sutherland (2010): It has normally been assumed that ribonucleotides arose on the early Earth through a process in which ribose, the nucleobases, and phosphate became conjoined. However, 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. The route as operated thus far in the laboratory is associated with several steps, and the conditions for these steps are different. Furthermore, purification in between certain steps was carried out to make analysis of the chemistry easier. Clearly, these issues need to be addressed before the synthesis can be seen as geochemically plausible. 3

Brian J. Cafferty (2015): 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. 40 
Terence N. Mitchell (2008):  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. 41 Fazale Rana (2011): In order for a molecule to be a self-replicator, it has to be a homopolymer, of which the backbone must have the same repetitive units; they must be identical. In the prebiotic world, for what reason would the generation of a homopolymer be useful? 37

Consider that only random non-designed events could account for the generation, which seems rationally extremely unlikely, if not impossible. The chance for that alone occurring by coincidence is extremely remote. 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 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 the formation of a bond between the nucleoside.  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 the 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-designed random events be able to attach the nucleic bases to the ribose and in a repetitive manner at the same, correct place?  

From nucleosides to nucleotides
Activated monomers are essential because polymerization reactions occur in an aqueous medium and are therefore energetically uphill in the absence of activation. A plausible energy source for polymerization remains an open question. Condensation reactions driven by cycles of anhydrous conditions and hydration would seem to be one obvious possibility but seem limited by the lack of specificity of the chemical bonds that are formed. 51

Libretexts: Phosphodiester bonds are central to most life on Earth, as they make up the backbone of the strands of DNA. 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 5-carbon ring carbohydrates (pentoses) over two ester bonds. 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. When a single phosphate or two phosphates known as pyrophosphates break away and catalyze the reaction, the phosphodiester bond is formed. Hydrolysis of phosphodiester bonds can be catalyzed by the action of phosphodiesterases which play an important role in repairing DNA sequences. 52

Prebiotic phosphodiester bond formation
An often-cited claim is that RNA polymerization could be performed on clay. Robert Shapiro wrote a critique in regards to prebiotic proposals of clay-catalyzed oligonucleotide synthesis (2006): 
An extensive series of studies on the polymerization of activated RNA monomers has been carried out by Ferris and his collaborators. A recent publication from this group concluded with the statement: “The facile synthesis of relatively large amounts of RNA oligomers provides a convenient route to the proposed RNA world. The 35–40 oligomers formed are both sufficiently long to exhibit fidelity in replication as well as catalytic activity”. The first review cited above had stated this more succinctly: “The generation of RNAs with chain lengths greater than 40 oligomers would have been long enough to initiate the first life on Earth”. Do natural clays catalyze this reaction? The attractiveness of this oligonucleotide synthesis rests in part on 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”. The native clays 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. Eventually the experimenters settled on Volclay, a commercially processed Wyoming montmorillonite provided by the American Colloid Company 11

Selecting the binding locations
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. 

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. 

Xaktly explains: 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. 46
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. 46

Eduard Schreiner (2011): 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.47

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 bio monomers would have had to exist. But none is known. Gerald Joyce wrote a science paper that was published in Nature magazine, in 1984. His findings 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 once God's guiding hand is excluded. How could that be a satisfying answer in face of the immense odds? 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. This is the way de Duve thought that Intelligent Design could be dismissed. This coming from a Nobel prize winner in medicine makes one wondering, 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.

Prebiotic base-pairing
In order to create a stable genome which was necessary for life to start, 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. 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 complimentary 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. A paper from Nature magazine, in 2016, demonstrates the complete lack of explanations despite decades of attempts to solve the riddle. Brian J. Cafferty and colleagues write:

The RNA World hypothesis presupposes that abiotic reactions originally produced nucleotides, the monomers of RNA and universal constituents of metabolism. However, compatible prebiotic reactions for the synthesis of complementary (that is, base pairing) nucleotides and mechanisms for their mutual selection within a complex chemical environment have not been reported. Despite decades of effort, the chemical origin of nucleosides and nucleotides (that is, nucleobases glycosylated with ribose and phosphorylated ribose) remains an unsolved problem.   They then proceed: Here we show that two plausible prebiotic heterocycles, melamine, and barbituric acid, form glycosidic linkages with ribose and ribose-5-phosphate in water to produce nucleosides and nucleotides in good yields. The data presented here demonstrate the efficient single-step syntheses of complementary nucleosides and nucleotides, starting with the plausible proto-nucleobases melamine and BA and ribose or R5P. 9

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3. John D Sutherland: Ribonucleotides 2010 Mar 10.
4. STANLEY L. MILLER: Rates of decomposition of ribose and other sugars: Implications for chemical evolution August 1995 
5. Irina V. Delidovich: Catalytic Formation of Monosaccharides: From the Formose Reaction towards Selective Synthesis 2014
6. Annabelle Biscans: Exploring the Emergence of RNA Nucleosides and Nucleotides on the Early Earth 2018 Dec; 8
7. Cornelia Meinert: Ribose and related sugars from ultraviolet irradiation of interstellar ice analogs 2016 Apr 8
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10. Prof. Dr. Oliver Trapp: Direct Prebiotic Pathway to DNA Nucleosides 26 May 2019
11.  A. G. Cairns-Smith Seven Clues to the Origin of Life: A Scientific Detective Story  1990
12. Robert Shapiro: [url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC20907/#:~:text=At 100%C2%B0C the,and T is 56 yr.]Prebiotic cytosine synthesis: A critical analysis and implications for the origin of life[/url] April 13, 1999
13. SAbby Vogel Robinson: Study: Adding UV light helps form ?Missing G? of RNA building blocks June 14, 2010
14. R Shapiro The prebiotic role of adenine: a critical analysis 1995 Jun;25
15. F H Westheimer:Why nature chose phosphates[/size]  1987 Mar 6
16. Prof. Gaspar Banfalvi: Why Ribose Was Selected as the Sugar Component of Nucleic Acids 28 Mar 2006
17. Steven A. Benner: SYNTHETIC BIOLOGY 01 July 2005
18. J.Oró: Synthesis of adenine from ammonium cyanide  June 1960
19. James P. Ferris and L. E. Orgel: Studies in Prebiotic Synthesis. I. Aminomalononitrile and 4-Amino-5-cyanoimidazole”” 1966 Aug 20
20. Annabelle Biscans: Exploring the Emergence of RNA Nucleosides and Nucleotides on the Early Earth 6 November 2018
21. Christian de Duve: Singularities: Landmarks on the Pathways of Life 2005
22. Guanine
23. Yasuhiro Oba: Identifying the wide diversity of extraterrestrial purine and pyrimidine nucleobases in carbonaceous meteorites 26 April 2022
24. Anil Oza: Could the Blueprint for Life Have Been Generated in Asteroids? Apr 26, 2022
25. Ben K. D. Pearce: Origin of the RNA world: The fate of nucleobases in warm little ponds October 2, 2017
26. R. Krishnamurthy: Experimentally investigating the origin of DNA/RNA on early Earth 12 December 2018
27. J.D. Sutherland, and Jack W. Szostak: Chemoselective Multicomponent One-Pot Assembly of Purine Precursors in Water November 2, 2010
28. James Urquhart Insight into RNA origins May 13, 2009
29. Caitlin McDermott-Murphy: First building blocks of life on Earth may have been messier than previously thought January 22, 2020
30. Jack W. Szostak* A Model for the Emergence of RNA from a Prebiotically Plausible Mixture of Ribonucleotides, Arabinonucleotides, and 2′-Deoxynucleotides January 8, 2020
31. Florian M. Kruse: Prebiotic Nucleoside Synthesis: The Selectivity of Simplicity 19 May 2020
32. Hidenori Okamura: A one-pot, water compatible synthesis of pyrimidine nucleobases under plausible prebiotic conditions 07 Jan 2019
33. SIDNEY W. FOX Synthesis of Uracil under Conditions of a Thermal Model of Prebiological Chemistry 16 Jun 1961
34. Leslie E Orgel: Prebiotic chemistry and the origin of the RNA world Mar-Apr 2004
35. Cornelia Meinert: Ribose and related sugars from ultraviolet irradiation of interstellar ice analogs 2016 Apr 8
36. Saidu lIslam: Prebiotic Systems Chemistry: Complexity Overcoming Clutter  13 April 2017
37. Fazale Rana: Creating Life in the Lab: How New Discoveries in Synthetic Biology Make a Case for the Creator February 1, 2011
38. Origin-of-Life Expert Jokes about Becoming a Creationist   11/05/2004
39. Norio Kitadai: Origins of building blocks of life: A review July 2018
40. Brian J. Cafferty: Was a Pyrimidine-Pyrimidine Base Pair the Ancestor of Watson-Crick Base Pairs? Insights from a Systematic Approach to the Origin of RNA 23 April 2015
41. Terence N. Mitchell: The “RNA World” 2008
42. Emily Singer New Twist Found in the Story of Life’s Start OCTOBER 11, 2016
43. Gerald F Joyce: The Origins of the RNA World 2012 May; 4
44. Gaspar Banfalvi: Ribose Selected as Precursor to Life 30 Jan 2020
45. Roger D. Blandford: The Chiral Puzzle of Life 2020
46. Jim Cleaves II: Encyclopedia of Astrobiology: Formose Reaction 2011
47. Steven A. Benner: The ‘‘Strong’’ RNA World Hypothesis: Fifty Years Old    2013 Apr;13
48. Steven A. Benner: Asphalt, Water, and the Prebiotic Synthesis of Ribose, Ribonucleosides, and RNA March 28, 2012
49. Rich Deem: Origin of life: latest theories/problems June 2001
50. Change Laura Tan, Rob

1. Change Laura Tan, Rob Stadler: The Stairway To Life: An Origin-Of-Life Reality Check  March 13, 2020 
2. Saidu lIslam: Prebiotic Systems Chemistry: Complexity Overcoming Clutter  13 April 2017
3. David Deamer: Bioenergetics and Life's Origins 2010 Feb; 2
4. [url=https://chem.libretexts.org/Courses/Sacramento_City_College/SCC%3A_Chem_309_-_General_Organic_and_Biochemistry_(Bennett)/Text/13%3A_Functional_Group_Reactions/13.10%3A_Phosphoester_Formation#:~:text=an ester bonds.-,Phosphodiesters,the strands of nucleic acid.]Phosphoester Formation[/url]
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18. Rob Stadler: Long Story Short — A Strikingly Unnatural Property of Biopolymers December 1, 2021
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30. F H Westheimer: Why nature chose phosphates  1987 Mar 6
31. Dr. Rafał Wieczorek: Formation of RNA Phosphodiester Bond by Histidine-Containing Dipeptides 18 December 2012
32. Robert P. Bywater writes in: On dating stages in prebiotic chemical evolution 15 February 2012
33. Charles W Carter, Jr: Interdependence, Reflexivity, Fidelity, Impedance Matching, and the Evolution of Genetic Coding  24 October 2017
34. Harris Bernstein: Origin of DNA Repair in the RNA World October 12th, 2020
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36. Pekka Teerikorpi: The Evolving Universe and the Origin of Life: The Search for Our Cosmic Roots2009
37. Jonathan Wells: The Politically Incorrect Guide to Darwinism and Intelligent Design August 21, 2006
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41. Gerald F. Joyce A cross-chiral RNA polymerase ribozyme 29 October 2014
42. G. F. Joyce: Chiral selection in poly(C)-directed synthesis of oligo(G) 16 August 1984
43. Suzan Mazur: Pier Luigi Luisi: Origin of Life Mindstorms Needed 19 December 2012
44. T M Tarasow: RNA-catalysed carbon-carbon bond formation 1997 Sep 4
45. Steven A. Benner: Asphalt, Water, and the Prebiotic Synthesis of Ribose, Ribonucleosides, and RNA March 28, 2012
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49. Timothy J Wilson: The potential versatility of RNA catalysis 2021 May 5

HAROLD B. WHITE, III (1975): Coenzymes are complex organic molecules that are essential for many enzyme-catalyzed reactions. At least 52% of the nearly 1750 enzymes recently cataloged (IUPAC-IUB, 1972) require a coenzyme for activity. I propose that coenzymes are the surviving vestiges of nucleic acid enzymes which preceded the evolution of ribosomal protein synthesis. 34

If the RNA world were true, ribozymes would have had to catalyze a wide range of catalytic reactions which subsequently were substituted by proteins. About half would only obtain the necessary catalytic activity by recruiting and employing cofactors and coenzymes ( which, as we see, also depend on complex biosynthesis pathways, and alternative non-enzymatic emergence would be very unlikely).  It is as if a Software engineer had to learn to become a mechanical engineer and assemble complex machines. There is no evidence that RNAs, made of just four different building blocks ( the four nucleobases), were ever able to catalyze the widely different enzymatic and metabolic reactions required for life to thrive. There is no evidence, that that somehow, prebiotic shuffling created a pool of millions of repetitive complex nucleotides, all with the repetitive configuration of purine and pyrimidine bases. There is no chemical logic that makes it appear plausible, that a gradual chemical evolutionary process would have promoted the emergence of an RNA world, followed by an RNA-peptide world. There is a wide unexplained gap between the RNA world, and the modern DNA - RNA - protein state of affairs in modern cells. Can this gap be bridged with new hypotheses and the advance in abiogenesis investigations? That prediction looks rather unlikely. Only time will tell. 
 
Solving a chicken & egg problem?
Supposedly, the RNA world hypothesis solved a long-standing chicken & egg, or catch22 problem ( J.Wells [2006]: In Joseph Heller’s novel about World War II, Catch-22, an aviator could be excused from combat duty for being crazy. But a rule specified that he first had to request an excuse, and anyone who requested an excuse from combat duty was obviously not crazy, so such requests were invariably denied. The rule that made it impossible to be excused from combat duty was called “Catch-22.”  ) In 1965, Sidney Fox wrote a scientific article, asking: How, when no life existed, did substances come into being which today are absolutely essential to living systems, yet which can only be formed by those systems?  He was referring to a problem, outlined by Jordana Cepelewicz (2017): For scientists studying the origin of life, one of the greatest chicken-or-the-egg questions is: Which came first — proteins or nucleic acids like DNA and RNA? 33 This problem arises because DNA and RNA direct the synthesis of enzymes and proteins. But proteins synthesize the making of RNA and DNA. 

Jessica C. Bowman (2015) claimed: The RNA World Hypothesis resolves the putative chicken and egg dilemma: which came first, polynucleotide or polypeptide? The simultaneous emergence from whole cloth of two functional biopolymers, one encoding the other, seems improbable. A single type of ancestral biopolymer (polynucleotide), performing multiple roles, appears to be characterized by high parsimony. A ‘‘Polymer Transition’’, a progression of biology from one polymer type (polynucleotide) to two polymer types (polynucleotide and polypeptide), is consistent with an expectation that ancient biology transitioned from simple to complex. 32

Under naturalism, the only possible explanation for the complexity seen in biochemistry is gradualism: From the simple to the complex. Gradually moving from chemistry to biology. A sudden appearance of all the complex interdependent intricacies observed in the living cannot be explained by a biochemical Big bang. It is untenable. Therefore, under the framework of philosophical naturalism, answers have to be found that confer with the gradualistic scenario. Only the model of intelligent design permits the hypothesis of instant creation by an intelligent agency. Giving up gradualism means giving up naturalism. 

Eugene V Koonin (2007): The origin of the translation system is, arguably, the central and the hardest problem in the study of the origin of life, and one of the hardest in all evolutionary biology. The problem has a clear catch-22 aspect: high translation fidelity hardly can be achieved without a complex, highly evolved set of RNAs and proteins but an elaborate protein machinery could not evolve without an accurate translation system. 13

Paul C. W. Davies (2013): Because of the organizational structure of systems capable of processing algorithmic (instructional) information, it is not at all clear that a monomolecular system, where a single polymer plays the role of catalyst and informational carrier, is even logically consistent with the organization of information flow in living systems because there is no possibility of separating information storage from information processing (that being such a distinctive feature of modern life). As such, digital-first systems (as currently posed) represent a rather trivial form of information processing that fails to capture the logical structure of life as we know it.  The real challenge of life's origin is thus to explain how instructional information control systems emerge naturally and spontaneously from mere molecular dynamics. 15

Self-replication in the RNA world
Despite the current celebrity status, there are several reasons that raise doubts that RNAs would self-assemble into ribozyme polymerases with function-bearing sequences, obtaining the right chemical structures with autocatalytic properties, and being apt to start self-replication. 

Harold S Bernhardt (2012): The following objections have been raised to the RNA world hypothesis: (i) RNA is too complex a molecule to have arisen prebiotically; (ii) RNA is inherently unstable; (iii) catalysis is a relatively rare property of long RNA sequences only; and (iv) the catalytic repertoire of RNA is too limited. 12

Since the various problems of prebiotic RNA monomers have been outlined in the previous chapter, we will address now the issues with RNA self-replication.  Steven Benner (2013): Catalysis and genetics place contradicting demands on any single molecular system asked to do both. For example, catalytic molecules should fold, to surround a transition state. Genetic molecules should not fold, to allow them to template the synthesis of their complements. Catalytic molecules should have many building blocks, to create versatile catalytic potential. Genetic molecules should have few building blocks, to ensure that they are copied with high fidelity 11

Jack W Szostak (2012): The first RNA World models were based on the concept of an RNA replicase - a ribozyme that was a good enough RNA polymerase that it could catalyze its own replication. Although several RNA polymerase ribozymes have been evolved in vitro, the creation of a true replicase remains a great experimental challenge. 6

Hannes Mutschler (2019): It has not yet been possible to demonstrate robust and continuous RNA self-replication from a realistic feedstock (i.e. activated mono- or short mixed-sequence oligonucleotides). In the case of ribozymes, only ‘simple’ ligation or recombination-based RNA replication from defined oligonucleotides has been demonstrated. Such systems have only a limited ability to transmit heritable information and so are not capable of open-ended evolution — the ability to indefinitely increase in complexity like living systems. Open-ended evolution requires that a replicase must at least be able to efficiently copy generic sequences longer than that required to encode its own function. RNA in isolation (including ribozymes) is simply not sufficient to catalyze its own replication, and substantial help from either other molecules or the environment is essential. 7

The annealing problem
Jordana Cepelewicz (2019): As a first step toward making a copy of itself, a single strand of RNA can take up complementary nucleotide building blocks from its surroundings and stitch them together. But the paired RNA strands then tend to bind to each other so tightly that they don’t unwind without help, which prevents them from acting as either catalysts or templates for further RNA strands. “It’s a real challenge,” Sutherland said. “It’s held the field back for a long time.” 8

Gerald F. Joyce (2018): Because the product of template copying is a double-stranded RNA, there must be some means of either strand separation or strand displacement synthesis. Transient temperature fluctuations could lead to thermal strand separation, but long RNA duplexes (≥30 base pairs) are difficult to denature thermally. 10

In modern cells, ribonuclease H enzymes destroy annealed RNAs but evidently, they were not around on prebiotic earth.

The Eigen paradox
Jaroslaw Synak (2022): Another challenge is the maintenance of genetic information in RNA sequences over many rounds of imperfect replication. In order to survive, RNA polymerase must be copied faster than it is hydrolyzed and accurately enough to preserve its function. In the early stages of molecular evolution, due to the lack of reliable replication mechanisms, the mutation rate was likely very high and the critical amount of information could not have been stored in long RNA sequences; on the other hand, the short ones could not be efficient enzymes. Maynard Smith estimated that the maximum length of the RNA replicase is approximately 100 nucleotides, assuming nonenzymatic replication with a copying fidelity of one base of up to 0.99. In order to further increase this length, the copying fidelity would have to be increased, which requires the presence of specific enzymes. This is known as Eigen’s paradox and is often equivalently formulated as: no enzymes without a large genome and no large 5

Indeed. But the problem is not only to maintain genetic information but for the first replicator to obtain it in the first place!

Natalia Szostak (2017): Researchers have performed many attempts to create RNA polymerase ribozyme, recently resulting in a cross-chiral RNA polymerase ribozyme and a system of cooperative RNA replicators, as well as RNA polymerase ribozyme that is able to synthesize structured functional RNAs, including aptamers and ribozymes. However, these molecules are too large to be maintained in a quasispecies population, as they exceed the 100 nucleotide error threshold, which is the maximum length polynucleotide molecule that can be accurately replicated without high fidelity polymerases. Eigen suggested hypercycles as a solution to the error threshold problem mentioned above. However, even if the traditional hypercycle model formulation based on ordinary differential equations is ecologically stable, it is proved to be evolutionarily unstable. To evolve life as we know it, separation of the roles performed by replicases, information storage, and replication of the information, into two molecules appears to be one of the crucial events that had to occur early in the stages leading to life. 4

A remarkable admission !!

Sami EL Khatib (2021): Countless challenges are faced by an RNA self-replicating cycle; for it to be a fully chemically and  enzymatically free reaction, the cycle loses rate and fidelity, so much that it does not even reach the critical threshold for the sustenance of life, meaning the RNA nucleotides break apart faster than the incorporation of nucleotides takes place, thus is the case when experimenting with modern substrates, that do not leak out of cells and are very polar with the regularly known triphosphate ester, this is advantageous to the modern cell where it uses enzymes to catalyze the release of di-phosphate, but not for the primitive cell as the substrates are found in the environment and require continuous dynamic exchange. The RNA world hypothesis has been criticized mostly because of the belief that long RNA sequences are needed for the catalytic function of RNA. These long sequences are enormous and are needed to isolate the catalytic and biding functions of the overall ribozyme. For example the best ribozyme replicase created so far, which is able to replicate an impressive 95-nucleotide stretch of RNA, is ~190 nucleotides in length, which is by far too large a number to have risen in any random assembly, thus in vitro selection experiments had to be designed where 10,000,000,000,000 – 1,000,000,000,000,000 of randomized RNA molecules are required as the starting point for the isolation of ribozymic and/or binding activity. This experiment clearly contradicts the probable prebiotic situation. 14

Eugene Koonin (2012):  The primary incentive behind the theory of self-replicating systems that Manfred Eigen outlined was to develop a simple model explaining the origin of biological information and, hence, of life itself. Eigen’s theory revealed the existence of the fundamental limit on the fidelity of replication (the Eigen threshold): If the product of the error (mutation) rate and the information capacity (genome size) is below the Eigen threshold, there will be stable inheritance and hence evolution; however, if it is above the threshold, the mutational meltdown and extinction become inevitable (Eigen, 1971). The Eigen threshold lies somewhere between 1 and 10 mutations per round of replication; regardless of the exact value, staying above the threshold fidelity is required for sustainable replication and so is a prerequisite for the start of biological evolution. Indeed, the very origin of the first organisms presents at least an appearance of a paradox because a certain minimum level of complexity is required to make self-replication possible at all; high-fidelity replication requires additional functionalities that need even more information to be encoded. However, the replication fidelity at a given point in time limits the amount of information that can be encoded in the genome. What turns this seemingly vicious circle into the (seemingly) unending spiral of increasing complexity—the Darwin-Eigen cycle.  The crucial question in the study of the origin of life is how the Darwin-Eigen cycle started—how was the minimum complexity that is required to achieve the minimally acceptable replication fidelity attained? In even the simplest modern systems, such as RNA viruses with the replication fidelity of only about 10^3 and viroids that replicate with the lowest fidelity among the known replicons (about 10^2), replication is catalyzed by complex protein polymerases. The replicase itself is produced by translation of the respective mRNA(s), which is mediated by the immensely complex ribosomal apparatus. Hence, the dramatic paradox of the origin of life is that, to attain the minimum complexity required for a biological system to start on the Darwin-Eigen spiral, a system of a far greater complexity appears to be required. How such a system could evolve is a puzzle that defeats conventional evolutionary thinking, all of which is about biological systems moving along the spiral; the solution is bound to be unusual.

When considering the origin of the first life forms, one faces the proverbial chicken-and-egg problem: What came first, DNA or protein, the gene or the product? In that form, the problem might be outright unsolvable due to the Darwin-Eigen paradox: To replicate and transcribe DNA, functionally active proteins are required, but production of these proteins requires accurate replication, transcription, and translation of nucleic acids. If one sticks to the triad of the Central Dogma, it is impossible to envisage what could be the starting material for the Darwin-Eigen cycle. Even removing DNA from the triad and postulating that the original genetic material consisted of RNA (thus reducing the triad to a dyad), although an important idea, does not help much because the paradox remains. For the evolution toward greater complexity to take off, the system needs to somehow get started on the Darwin-Eigen cycle before establishing the feedback between the (RNA) templates (the information component of the replicator system) and proteins (the executive component). The brilliantly ingenious and perhaps only possible solution was independently proposed by Carl Woese, Francis Crick, and Leslie Orgel in 1967–68: neither the chicken nor the egg, but what is in the middle—RNA alone. The unique property of RNA that makes it a credible—indeed, apparently, the best—candidate for the central role in the primordial replicating system is its ability to combine informational and catalytic functions. Thus, it was extremely tempting to propose that the first replicator systems—the first life forms—consisted solely of RNA molecules that functioned both as information carriers (genomes and genes) and as catalysts of diverse reactions, including, in particular, their own replication and precursor synthesis. This bold speculation has been spectacularly boosted by the discovery and subsequent study of ribozymes (RNA enzymes), which was pioneered by the discovery by Thomas Cech and colleagues in 1982 of the autocatalytic cleavage of the Tetrahymena rRNA intron, and by the demonstration in 1983 by Sydney Altman and colleagues that RNAse P is a ribozyme. Following these seminal discoveries, the study of ribozymes has evolved into a vast, expanding research area. 

Despite all invested effort, the in vitro evolved ribozymes remain (relatively) poor catalysts for most reactions; the lack of efficient, processive ribozyme polymerases seems particularly troubling. An estimate based on the functional tolerance of well-characterized ribozymes to mutations suggest that, at fidelity of 10^3 errors per nucleotide per replicase cycle (roughly, the fidelity of the RNA-dependent RNA polymerases of modern viruses), an RNA “organism” with about 100 “genes” the size of a tRNA (80 nucleotides) would be sustainable. Such a level of fidelity would require only an order of magnitude improvement over the most accurate ribozyme polymerases obtained by in vitro selection 3

Lack of prebiotic RNA repair mechanisms
Harris Bernstein (2020): Persistence and replication of even the simplest forms of RNA life must have depended on preserving the information content of the RNA genome from damage (a form of informational noise). Damage to the RNA genome likely occurred in a variety of ways including spontaneous hydrolysis, exposure to UV light and exposure to reactive chemicals. 9

Where did the energy come from?
Jack Szostak, interviewed by Suzan Mazur (2014): The problem is RNA falls apart. The activated nucleotides we use to do the non-enzymatic replication -- they react with water, so they fall apart. There needs to be a way to bring energy back into the system to essentially keep the battery charged. To keep all the nucleotides activated and to keep things running. 1

PHILIP BALL (2020): It’s an alluring picture – catalytic RNAs appear by chance on the early Earth as molecular replicators that gradually evolve into complex molecules capable of encoding proteins, metabolic systems and ultimately DNA. But it’s almost certainly wrong. For even an RNA-based replication process needs energy: it can’t shelve metabolism until later. And although relatively simple self-copying ribozymes have been made, they typically work only if provided with just the right oligonucleotide components to work on. What’s more, sustained cycles of replication and proliferation require special conditions to ensure that RNA templates can be separated from copies made on them. Perhaps the biggest problem is that self-replicating ribozymes are highly complex molecules that seem very unlikely to have randomly polymerized in a prebiotic soup. And the argument that they might have been delivered by molecular evolution merely puts the cart before the horse. The problem is all the harder once you acknowledge what a complex mess of chemicals any plausible prebiotic soup would have been. It’s nigh impossible to see how anything lifelike could come from it without mechanisms for both concentrating and segregating prebiotic molecules – to give RNA-making ribozymes any hope of copying themselves rather than just churning out junk, for example. In short, once you look at it closely, the RNA world raises as many questions as it answers.  The best RNA polymerase the researchers obtained this way had a roughly 8% chance of inserting any nucleotide wrongly, and any such error increased the chance that the full chain encoded by the molecule would not be replicated. What’s more, making the original class I ligase was even more error-prone and inefficient – there was a 17% chance of an error on each nucleotide addition, plus a small chance of a spurious extra nucleotide being added at each position. These errors would be critical to the prospects of molecular evolution since there is a threshold error rate above which a replicating molecule loses any Darwinian advantage over the rest of the population – in other words, evolution depends on good enough replication. Fidelity of copying could thus be a problem, hitherto insufficiently recognized, for the appearance of a self-sustaining, evolving RNA-based system: that is, for an RNA world. Maybe this obstacle could have been overcome in time. But my hunch is that any prebiotic molecule will have been too inefficient, inaccurate, dilute and noise-ridden to have cleared the hurdle. 2

An RNA world could not explain the origin of the genetic code
Susan Lindquist (2010): An RNA-only world could not explain the emergence of the genetic code, which nearly all living organisms today use to translate genetic information into proteins. The code takes each of the 64 possible three-nucleotide RNA sequences and maps them to one of the 20 amino acids used to build proteins. 29

Without amino acids, there could not be an assignment. 64 trinucleotide codons are assigned to 20 amino acids. Both had to be present, in order for this assignment to occur. But having both would not be enough either. In reality, the entire system had to be created from the get-go, fully developed, and operational from the beginning. That led Fujio Egami (1981) to present a " working hypothesis on the interdependent genesis of nucleotide bases, protein amino acids, and the primitive genetic code: the primitive genetic code was dependent upon the concentration of different nucleotide bases and amino acids coexisting in the primeval environments and upon the selective affinity between bases and amino acids." 30
 
Charles W Carter, Jr (2017): Computational and structural modeling argue that some mutual, interdependent processes embedded information into proteins and nucleic acids.

While talking about evolutionary modification, Egami was probably not aware that an interdependent system cannot be the product of evolutionary change. An interdependent system must be right all at once, right from the start. Stepwise, gradual evolution of the system is not possible, since intermediate stages would confer no advantage, nor function. Mapping nucleotides to amino acids is only possible if all players are there. 31

The RNA-peptide world
The RNA-peptide world tries to build a bridge between the replication first, and metabolism first scenarios, advancing the RNA world and combining it with catalytic peptides and primitive metabolism.

Stephen D. Fried (2022): Diverse lines of research in molecular biology, bioinformatics, geochemistry, biophysics, and astrobiology provide clues about the progression and early evolution of proteins, and lend credence to the idea that early peptides served many central prebiotic roles before they were encodable by a polynucleotide template, in a putative ‘peptide-polynucleotide stage’. 23

The presupposition is that a result of chemical prebiotic conditions permitted the emergence of activated ribonucleotides and amino acids.  The proposal hypothesizes that RNAs started to interact and get into a relationship with small peptides ( small amino acid strands) right from the beginning, rather than everything starting exclusively with RNAs, that later would transition to mutually beneficial interaction with amino acids.  In modern cells, DNA that stores the genetic data using the genetic code is transcribed into messenger RNA (mRNA), subsequently translated in the ribosome apparatus into functional amino acid sequences, which form polypeptides, and in the end, proteins. The core problem is the origin of the codon-amino acid assignment through the genetic code. The RNA-peptide world attempts to address this current state of affairs, starting with an RNA-peptide world, which constitutes the first step to arrive at the end of the current solution, where the sophisticated translation is performed through the ribosome.    

Charles W. Carter, Jr. (2015): In the RNA-world scenario, the necessary catalysts were initially entirely RNA-based and did not include genetically encoded proteins. IN the RNA-peptide world, the idea that coded peptides functioned catalytically in the early stages of the origin of life directly contradicts the second central tenet of the “RNA World” scenario.  The important distinction between this scenario and the RNA World hypothesis is that the requisite specificity is low in the initial stages of the former but unacceptably high in the latter. Low specificity processes occur with greater frequency and hence are more likely to have occurred first. The unavailability of activated amino acids was the most critical barrier to the emergence of protein synthesis. 16

Dave Speijer (2015): Very small RNAs (versatile and stable due to base-pairing) and amino acids, as well as dipeptides, coevolved. The “RNA world” hypothesis is seen as one of the main contenders for a viable theory on the origin of life. Relatively small RNAs have catalytic power, RNA is everywhere in present-day life, the ribosome is seen as a ribozyme, and rRNA and tRNA are crucial for modern protein synthesis. However, this view is incomplete at best. The modern protein-RNA ribosome most probably is not a distorted form of a “pure RNA ribosome” evolution started out with. Though the oldest center of the ribosome seems “RNA only”, we cannot conclude from this that it ever functioned in an environment without amino acids and/or peptides. Very small RNAs (versatile and stable due to base-pairing) and amino acids, as well as dipeptides, coevolved. Remember, it is the amino group of aminoacylated tRNA that attacks peptidyl-tRNA, destroying the bond between peptide and tRNA. This activity of the amino acid part of aminoacyl-tRNA illustrates the centrality of amino acids in life. With the rise of the “RNA world” view of early life, the pendulum seems to have swung too much towards the ribozymatic part of early biochemistry. The necessary presence and activity of amino acids and peptides is in need of highlighting. We argue that an RNA world completely independent of amino acids never existed.

Indeed, I agree, that an RNA world never existed. But did an RNA-peptide world?

Speijer: The idea of an independent RNA world without oligopeptides or amino acids stabilizing structures and helping in catalysis does not seem a viable concept. On the other hand, the idea of catalytic protein existing without RNA storing the polypeptide sequences, which have catalytic activity, and organizing the production of these sequences, also does not seem a viable concept. Here we argue for a “coevolutionary” theory in which amino acids and (very small) peptides, as well as small RNAs, existed together and where their separate abilities not only reinforced each other’s survival but allowed life to more quickly climbing the ladder of complexity.

Every naturalistic approach works only from the simple to the complex in a slow, gradual manner. Even if not linear but with ups and downs, the outcome is always that there is more functional complexity at the end. That is as well Speijers proposal: "Starting with small molecules (easily) derived from prebiotic chemistry, we will try to reconstruct a possible history in which every stage of increased complexity arises from the previous more simple stage because specific nucleotide/amino acid (RNA/peptide) interactions allowed it do so." Observe how Speijer introduces teleonomy into the explanation when claiming: their separate abilities reinforced each other’s survival . As if RNAs and amino acids operated or behaved with the "aim" or purpose of arriving and keeping a state of affairs, that wasn't there yet. RNAs and amino acids on their own are not alive, and have no aim to enter the trajectory to "help" the arrival of the state of affairs of having something alive, part of the living. Molecules have no innate drive or "urge" to keep a specific state, to get out of thermodynamic equilibrium, that would favor a future outcome, the gradual complexification that would, in the end, result in the existence of self-replicating cells.

Speijer: We now come at a crucial and, we have to admit, somewhat theoretical juncture: coevolution is illustrated by the presumption that RNAs could not persist without peptide protection, that very short (very early) peptides were made more abundant by RNA-producing them, and that they co-evolve forming longer RNAs and peptides. This would constitute an RNA/peptide world of ribozymes and short oligopeptides. These oligopeptides had RNA protection functions (DADVDGD being the obvious ancestor sequence of the universal RNA polymerase active site sequence NADFDGD) This motif (Asn-Ala-Asp-Phe-Asp-Gly-Asp) is a specific stretch of amino acids that is central in all cellular life. RNA polymerases catalyze the transcription from DNA to mRNA. Dennis R. Salahub (2008): Most known RNA polymerases (RNAPs) share a universal heptapeptide, called the NADFDGD motif. The crystal structures of RNAPs indicate that in all cases this motif forms a loop with an embedded triad of aspartic acid residues. This conserved loop is the key part of the active site. 17

The odds to get this sequence randomly is one in 20^7 or one in 10^10, that is taking a pool of 20 selected amino acids used in life would have to be shuffled 10 billion times to get this specified functional sequence. Not forgetting, that it is incorporated in a much longer polymer sequence that also has to be functional, embedded, and working in a joint venture with other polymer subunit strands of RNA polymerase. A far fetch.

Kunnev (2018): The hypothesis assumes that ribonucleotides would polymerize leading to very short RNAs from 2 to about 40 bases. The polymerization would incorporate random sequences and random 3D structures. The process would preserve mostly stable ones. Wet-Dry cycles could facilitate the process of RNA polymerization. Compartmentalization is another important factor since most of the described events are unlikely to occur in very low concentrations. Some level of environmental separation would be expected, for example, micro-chambers out of porous surface of rocks or lipid vesicles or both. Surface adsorption might have facilitated RNA-RNA interactions, RNA-lipids interactions and some beneficial chemical reactions. Thus, clay surfaces have been shown to promote encapsulation of RNA into vesicles and grow by incorporating fatty acid supplied as micelles and can divide without dilution of their contents.  At temperatures between 1°C and to denaturation (about 55°C) temperature, short random RNA oligos would get stabilized via intra and intermolecular hybridization based on Watson-Crick base pairing, forming complexes of various 3D shape and size. Larger hybridized regions would confer greater stability and would be selected for. Highly self-complementary RNAs would be unlikely to exist, forcing intermolecular hybridization of short sequences and the emergence of complexes of several RNA oligos. The formation of RNA complexes also assumes a thermal cycle that would drive the process by sequential denaturation (~55–100°C) and re-annealing (<55°C) phases. Frequent repetition of the thermal cycle and stability selection would favor accumulation of complexes with higher degree of complementarity and higher GC content. Non-enzymatic aminoacylation between 2′ or 3′ positions of ribose and activated amino acids could occur. In addition, ribozymes capable of amino acid transfer from one RNA to another have been selected under laboratory conditions and similar molecules could have participated in aminoacylation of RNAs. Aminoacylated RNAs would be involved in complex formation, bringing some of the aminoacylated RNA 3′-ends in close proximity. This would promote peptide bond formation between two adjacent amino acids, most likely with the assistance of wet/dry natural cycles. All amino acids would have statistically equal probability to aminoacylate RNA. At that stage, any RNA molecule could be aminoacylated and could serve as a template. 18

That means, any available amino acid nearby could be involved in the reaction - inclusive amino acids not used in life, and they could be attached anywhere to the RNA molecule. There is also no restriction in regards of possible RNA configurations with any sort of nucleobases. There is no mechanism that would prevent other than the nucleobases used in life to be involved in the reactions.  It would result simply in a disordered random accumulation of RNA-peptides. 

Kunnev: We presume that following this initial stage all components of the translation system would co-evolve in a stepwise way. Specialization of ribosomal Large Subunit—LSU will start with evolution of peptidyl transferase center (PTC). The evolution of peptides to proteins would occur from small motif to domains and finally— folded proteins. 

Felix Müller (2022): The ability to grow peptides on RNA with the help of non-canonical vestige nucleosides offers the possibility of an early co-evolution of covalently connected RNAs and peptides, which then could have dissociated at a higher level of sophistication to create the dualistic nucleic acid–protein world that is the hallmark of all life on Earth. It is difficult to imagine how an RNA world with complex RNA molecules could have emerged without the help of proteins and it is hard to envision how such an RNA world transitions into the modern dualistic RNA and protein world, in which RNA predominantly encodes information whereas proteins are the key catalysts of life.22

This story, when it comes to elucidating the trajectory from these small RNA-peptides, to fully developed proteins is very "sketchy" and superficial. This is a common modus operandi to uphold a story, that by looking closer, does not withstand scrutiny.

Charles Carter, structural biologist (2017): For life to take hold, the mystery polymer would have had to coordinate the rates of chemical reactions that could differ in speed by as much as 20 orders of magnitude. 24

Marcel Filoche (2019): Enzymes speed up biochemical reactions at the core of life by as much as 15 orders of magnitude. Yet, despite considerable advances, the fine dynamical determinants at the microscopic level of their catalytic proficiency are still elusive. Rate-promoting vibrations in the picosecond range, specifically encoded in the 3D protein structure, are localized vibrations optimally coupled to the chemical reaction coordinates at the active site. Remarkably, our theory also exposes a hitherto unknown deep connection between the unique localization fingerprint and a distinct partition of the 3D fold into independent, foldspanning subdomains that govern long-range communication. The universality of these features is demonstrated on a pool of more than 900 enzyme structures, comprising a total of more than 10,000 experimentally annotated catalytic sites. Our theory provides a unified microscopic rationale for the subtle structure-dynamics-function link in proteins. The intricate networks of metabolic cascades that power living organisms ultimately rest on the exquisite ability of enzymes to increase the rate of chemical reactions by many orders of magnitude. Although many molecular machines contain intrinsically disordered domains, the 3D fold is central to enzyme functioning. In particular, increasing evidence is accumulating in the literature in favor of the existence of specific fold-encoded motions believed to govern the relevant collective coordinate(s) that are coupled to the chemical transformation. These motions typically correspond to localized vibrations of the protein scaffold that contribute to the catalytic reaction, i.e., modes that, if impeded, would lead to a deterioration of the catalytic efficiency.

The more the function of a machine depends on its precise setup and arrangement respecting very limited tolerances, the more efforts have to be undertaken to achieve the required precision, demanding engineering solutions where nothing can be left to chance. That is precisely the case with proteins. There is an extraordinarily limited tolerance upon which proteins have to be engineered and designed, a requirement to achieve the necessary catalytic functions. That sets the bar for the cause to instantiate this state of affairs very high, for which random events are entirely inadequate!! The situation becomes even worse when we consider what Mathieu E. Rebeaud described as (2021): the challenge of reaching and maintaining properly folded and functional proteomes. Most proteins must fold to their native structure in order to function, and their folding is largely imprinted in their primary amino acid sequence. However, many proteins, especially large multidomain polypeptides, or certain protein types such as all-beta or repeat proteins, tend to misfold and aggregate into inactive species that may also be toxic. Life met this challenge by evolving employing molecular chaperones that can minimize protein misfolding and aggregation, even under stressful out-of-equilibrium conditions favoring aggregation. 25

Hays S. Rye (2013): Protein folding is a spontaneous process that is essential for life, yet the concentrated and complex interior of a cell is an inherently hostile environment for the efficient folding of many proteins. Some proteins—constrained by sequence, topology, size, and function—simply cannot fold by themselves and are instead prone to misfolding and aggregation. This problem is so deeply entrenched that a specialized family of proteins, known as molecular chaperones assists in protein folding. The bacterial chaperonin GroEL, along with its co-chaperonin GroES, is probably the best-studied example of this family of protein-folding machine. 27

Chaperones do bear no function unless there are misfolded proteins, that need to be re-folded in order to function. But non-functional proteins accumulating in the cell would be toxic waste and eventually kill the cell. So this creates another chicken & egg problem. What came first: Protein synthesis, or chaperones helping proteins to fold correctly? Consider as well, that, as Jörg Martin puts it (2000): The intracellular assembly of GroEL-type chaperonins appears to be a chaperone-dependent process itself and requires functional preformed chaperonin complexes !! 26 There are machines in the cell, that help other machines to be folded correctly, and these machines are also employed to help other machines to fold in order to be able to operate properly! Amazing!

Thorsten Hugel (2020): In a living cell, protein function is regulated in several ways, including post-translational modifications (PTMs), protein-protein interaction, or by the global environment (e.g. crowding or phase separation). While site-specific PTMs act very locally on the protein, specific protein interactions typically affect larger (sub-)domains, and global changes affect the whole protein non-specifically. Herein, we directly observe protein regulation under three different degrees of localization, and present the effects on the Hsp90 chaperone system at the levels of conformational steady states, kinetics and protein function. Interestingly using single-molecule FRET, we find that similar functional and conformational steady states are caused by completely different underlying kinetics. We disentangle specific and non-specific effects that control Hsp90’s ATPase function, which has remained a puzzle up to now. Lastly, we introduce a new mechanistic concept: functional stimulation through conformational confinement. Our results demonstrate how cellular protein regulation works by fine-tuning the conformational state space of proteins. 28

Susan Lindquist (2010): Cells also require a ubiquitin-proteasome system, targeting terminally misfolded proteins for degradation, and with translocation machineries to get proteins to their proper locations. These protein folding agents constitute a large, diverse, and structurally unrelated group. Many are upregulated in response to heat and are therefore termed heat shock proteins (HSPs).  HSP90 is one of the most conserved HSPs, present from bacteria to mammals, and is an essential component of the protective heat shock response. The role of HSP90, however, extends well beyond stress tolerance. Even in nonstressed cells, HSP90 is highly abundant and associates with a wide array of proteins (known as clients) that depend on its chaperoning function to acquire their active conformations. 20% of yeast proteins are influenced by Hsp90 function, making it the most highly connected protein in the yeast genome, and GroES mediates the folding of ~10% of proteins in E. coli.29

Short RNA-peptides, or peptides on their own, are not functional and are useless in a supposed "proto-cell" unless they have the right size and sequence, able to fold into the functional 3D conformation.  In face of this evidence, supposing and theorizing intermediate states and transitions of growing size and complexity over long periods of time until a functional state of affairs is achieved, is untenable. It opposes the evidence just described. Sophisticated exquisite mechanisms have to be instantiated from the get-go, to guarantee the right setup and folding of proteins of the full length.  Such a hypothesized transition is never to work and going to happen. These RNA-peptides would simply lay around, and then sooner or later disintegrate.  These explanations not including an intelligent agent are entirely inadequate to account for the origin of this kind of these high-tech engineering marvel implementations on a molecular scale!

George Church, Professor of Genetics, described the ribosome as "the most complicated thing that is present in all organisms". The peptidyl transferase center (PTC) is the core of the ribosome, where peptide bond formation occurs, which is a central catalytic reaction in life, where proteins are synthesized, and is as such of particular importance.  The process is so intriguingly complex, that a science paper in 2015 had to admit that: "The detailed mechanism of peptidyl transfer, as well as the atoms and functional groups involved in this process are still in limbo." 19 The PTC is a ribozyme, which means it is composed of ribosomal RNAs ( rRNAs). Francisco Prosdocimi (2020): The PTC region has been considered crucial in the understanding about the origins of life. It has been described as the most significant trigger that engendered a mutualistic behavior between nucleic acids and peptides, allowing the emergence of biological systems. The emergence of this proto-PTC is a prerequisite to couple a chemical symbiosis between RNAs and peptides. Of 1434 complete sequences of 23S ribosomal RNAs analyzed, it was demonstrated that site A2451 from the 23S rRNA, which is the catalytic site of the PTC, is essential for the peptide bond to occur, and is absolutely preserved in each and every analyzed sequence. The PTC is known to be a flexible and efficient catalyst as it is capable of recognizing different, specific substrates (20 different amino acids bind to aminoacyl-tRNAs) and polymerizing proteins at a similar rate. 20  

Sávio T.Farias (2014): Studies reveal that the PTC has a symmetrical structure comprising approximately 180 nucleotides. Molecular structure models suggest that the catalytic portion of the 23S rRNA entities of the symmetrical region possesses the common stem-elbow-stem (SES) structural motif. 21

Let's suppose that this structure would have emerged in an RNA-peptide world. Let's also not consider, that finding a functional sequence of 180 RNAs would vastly exceed the resources in sequence space, exhausting the maximum number of possible events in a universe that is 18 Billion years old (10^16 seconds) where every atom (10^80) is changing its state at the maximum rate of 10^40 times per second is 10^139. If we had such a core PTC, it would have no function whatsoever, unless all other players would be in place to perform translation from RNA to amino acids, having as well the genetic code implemented, and the entire chain from DNA to mRNA, to then coming to the events in translation. All these proposals, the RNA world, and the RNA-peptide world are based on silly pipe dreams - that they call theories when they are not more than ideas, based on fertile minds, and not results based on scientific evidence, experimentation, and tests in the lab. These are just invented scenarios - out of the need to keep an explanatory framework based on philosophical naturalism to find answers that do not require invoking a supernatural entity. All these proposals have been shown to be inadequate and doomed to failure.  Biological cells are too complicated, sophisticated, integrated, and functional in order to warrant the belief that they could have originated by unguided means - the ribosome is a prime example to conclude this.

1. Suzan Mazur: The Origin of Life Circus: A How To Make Life Extravaganza  November 30, 2014
2. PHILIP BALL: Flaws in the RNA world  12 FEBRUARY 2020
3. Eugene Koonin: The Logic of Chance: The Nature and Origin of Biological Evolution  31 agosto 2011
4. Natalia Szostak: Simulating the origins of life: The dual role of RNA replicases as an obstacle to evolution July 10, 2017
5. Jaroslaw Synak: RNA World Modeling: A Comparison of Two Complementary Approaches 11 April 2022
6. Jack W Szostak: The eightfold path to non-enzymatic RNA replication 03 February 2012
7. Hannes Mutschler: The difficult case of an RNA-only origin of life AUGUST 28 2019
8. Jordana Cepelewicz: Origin-of-Life Study Points to Chemical Chimeras, Not RNA September 16, 2019
9. Harris Bernstein: Origin of DNA Repair in the RNA World October 12th, 2020
10. Gerald F. Joyce: Protocells and RNA Self-Replication 2018
11. Steven A. Benner: The ‘‘Strong’’ RNA World Hypothesis: Fifty Years Old 2013 Apr;13
12. Harold S Bernhardt:[url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3495036/#:~:text=However%2C the following objections have,of RNA is too limited.] The RNA world hypothesis: the worst theory of the early evolution of life[/url] (except for all the others) 2012 Jul 13
13. Eugene V Koonin: On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization 2007 May 31
14. Sami EL Khatib: Assumption and Criticism on RNA World Hypothesis from Ribozymes to Functional Cells March 12, 2021
15. Paul C. W. Davies: The algorithmic origins of life 2013 Feb 6
16. Charles W. Carter, Jr. What RNA World? Why a Peptide/RNA Partnership Merits Renewed Experimental Attention 23 January 2015
17. Dennis R. Salahub: Characterization of the active site of yeast RNA polymerase II by DFT and ReaxFF calculations 08 April 2008
18. Dimiter Kunnev: Possible Emergence of Sequence Specific RNA Aminoacylation via Peptide Intermediary to Initiate Darwinian Evolution and Code Through Origin of Life 2018 Oct 2;8
19. Hadieh Monajemi: The P-site A76 2′-OH acts as a peptidyl shuttle in a stepwise peptidyl transfer mechanism 2015
20. Francisco Prosdocimi: The Ancient History of Peptidyl Transferase Center Formation as Told by Conservation and Information Analyses 2020 Aug 5
21. Sávio T.Farias: Origin and evolution of the Peptidyl Transferase Center from proto-tRNAs 2014
22. Felix Müller: A prebiotically plausible scenario of an RNA–peptide world 11 May 2022
23. Stephen D. Fried: Peptides before and during the nucleotide world: an origins story emphasizing cooperation between proteins and nucleic acids 09 February 2022
24. Jordana Cepelewicz: The End of the RNA World Is Near, Biochemists Argue December 19, 2017
25. Mathieu E. Rebeaud:  On the evolution of chaperones and cochaperones and the expansion of proteomes across the Tree of Life May 17, 2021
26. Jörg Martin: Assembly and Disassembly of GroEL and GroES Complexes 2000
27. Hays S. Rye: GroEL-Mediated Protein Folding: Making the Impossible, Possible 2013 Sep 25
28. Thorsten Hugel: Controlling protein function by fine-tuning conformational flexibility 2020 Jul 22
29. Susan Lindquist: HSP90 at the hub of protein homeostasis: emerging mechanistic insights 2010 Jul;11
30. F Egami: A working hypothesis on the interdependent genesis of nucleotide bases, protein amino acids, and primitive genetic code 1981 Sep;11
31. Charles W Carter, Jr: Interdependence, Reflexivity, Fidelity, Impedance Matching, and the Evolution of Genetic Coding 24 October 2017
32. Jessica C. Bowman: The Ribosome Challenge to the RNA World  20 February 2015
33. Jordana Cepelewicz: Life’s First Molecule Was Protein, Not RNA, New Model Suggests November 2, 2017
34. Coenzymes & Cofactors

My name is James Compton, science researcher and book author. When talking about the origin of life, many believe that the issue is still a scientifically open question, that science is working towards solving the problem, and a solution near the next corner. Lee Cronin, for example, made a prediction in 2011. Unfortunately, it didn't concretize.  There are many reasons, why intelligent guidance had to be involved in the process. In this video, I will expose one reason. One of the most popular hypotheses is that life started with the so-called RNA world. Before we continue, a quick elucidation of what life is.



As the shortest description, life is basically chemistry and information. In more detail, life consists of Reproduction, Metabolism, Nutrition, Complexity, Organization.  Growth and development. Information content. Hardware/software entanglement,   Permanence, and change.


Donald Prothero wrote in his book: The evolving earth published in 2019: The simplest scenario for the origin of living, self-replicating systems would be an “RNA world.” The very first self-replicating form of life would be a single-stranded RNA, perhaps enclosed in a lipid bilayer membrane and perhaps using simple carbohydrates for food storage. Using both its replication powers and enzymatic powers, it would make more copies of itself and perform the role of the proteins as well until later, more complex reactions involving many different proteins could evolve. Every year, more discoveries are made that add details to our understanding of the origin of life and the RNA world.

He starts his narrative with a single-stranded RNA. Here is the problem. In order for the RNA world to be true, one needs to start much earlier, namely with the origin of RNA itself. Only then, further questions can be asked, like how RNA polymerized, and eventually started self-replicating. 

A number of reasons have been given why a prebiotic synthesis of RNA, and even more, DNA, is too complex. 






In cells, the synthesis of RNA and DNA requires extremely complex energy-demanding, finely adjusted, monitored,  and controlled anabolic pathways. Since they were not extant prebiotically, RNA had to be synthesized spontaneously on early earth by abiotic alternative non-enzymatic pathways.  This is one of the major, among many other unsolved origin of life problems.


A recent article in the journal of the Royal Society claims that RNA, proteins and the genetic code that binds them each look like products of natural selection. I have no idea how they conclude that they seem the product of natural selection. To me, it indeed seems that these building blocks had to be selected, but nature has no intent, no goals, no aim to complexity molecules towards life. If a selection process was necessary, then it had to have another source, instead of nature.

Graham Cairns-Smith  lists several hurdles that would have to be overcome in his book: Genetic takeover, page 64:



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  nucleotides. In practice the discrimination required to make nucleotide parts cleanly, or to assemble them correctly, seems insufficient.

So powerful has been the effect of Miller’s experiment on the scientific imagination that to read some of the literature on the origin of life (including many elementary texts) you might think that it had been well demonstrated that nucleotides were probable constituents of a primordial soup and hence that prevital nucleic acid replication was a plausible speculation based on the results of experiments. There have indeed been many interesting and detailed experiments in this area. But the importance of this work lies, to my mind, not in demonstrating how nucleotides could have formed on the primitive Earth, but in precisely the opposite: these experiments allow us to see, in much greater detail than would otherwise have been possible, just why prevital nucleic acids are highly implausible. Let us consider some of the difficulties to make RNA & DNA.

In Genetic Takeover I listed 14 major hurdles that would have to be overcome for primed nucleotides to have been made on the primitive Earth - from the build-up of sufficient and separate concentrations of formaldehyde and cyanide to the final 'winding-up' of the nucleotides. In practice each of these processes would be subdivided into separate unit operations that would have to be suitably sequenced.



I think, to say that on average the 14 hurdles that I referred to in the making of primed nucleotides would each take 10 unit operations - that at least 140 little events would have to be appropriately sequenced. (If you doubt this, go and watch an organic chemist at work; look at all the things he actually does in bringing about what he would describe as 'one step' in an organic synthesis.) This is a huge number, represented approximately by a 1 followed by 109 zeros. This is the sort of number of trials that you would have to make to have a reasonable chance of hitting on the one outcome that represents success. Throwing one dice once a second for the period of the Earth's history would only let you get through about 10^15 trials.

An article published in 2014 summarizes the current status quo: The first, and in some ways the most important, problem facing the RNA World is the difficulty of prebiotic synthesis of RNA. This point has remained a focal point of the efforts of prebiotic chemists for decades. The ‘traditional’ thinking was that if one could assemble a ribose sugar, a nucleobase, and a phosphate, then a nucleotide could arise through the creation of a glycosidic bond and a phosphodiester bond. If nucleotides were then chemically activated in some form, then they could polymerize into an RNA chain. Each of these synthetic events poses tremendous hurdles for the prebiotic Earth, not to mention the often-invoked critique of the inherent instability of RNA in an aqueous solution. Thus, the issue arises of whether there could have been a single environment in which all these steps took place. Benner has eloquently noted that single-pot reactions of sufficient complexity lead to ‘asphaltization’ (basically, the production of intractable ‘goo’).


The asphalt problem has been outlined by Rob Stadler and Change Laura Tan in their book: Stairway to life: 



The asphalt problem has been outlined by Rob Stadler and Change Laura Tan in their book: Stairway to life: 




Even in a very short DNA of just two nucleotides, there are dozens of incorrect possible arrangements of the components, and only one correct arrangement. The probability of consistent arrangement decreases exponentially as the DNA lengthens. If natural processes could polymerize these monomers, the result would be chaotic “asphalt,” not highly organized, perfectly consistent biopolymers. Think about it — if monomers spontaneously polymerized within cells, the cell would die because all monomers would be combined into useless random arrangements.




And Steve Benner has made another observation, which means a death knell for the prebiotic synthesis or RNA: An enormous amount of empirical data has established, as a rule, that organic systems, given energy and left to themselves, devolve to give uselessly complex mixtures, “asphalts”. The literature reports (to our knowledge) exactly zero confirmed observations where evolution emerged spontaneously from a devolving chemical system. Further, chemical theories, including the second law of thermodynamics, bonding theory that describes the “space” accessible to sets of atoms, and structure theory requiring that replication systems occupy only tiny fractions of that space, suggest that it is impossible for any non-living chemical system to escape devolution to enter into the Darwinian world of the “living”. 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.



Another widespread myth is that RNA polymerization is something that has been demonstrated to be possible on clay. Robert Shapiro wrote a critique in regards to prebiotic proposals of clay-catalyzed oligonucleotide synthesis. An extensive series of studies on the polymerization of activated RNA monomers has been carried out by Ferris and his collaborators. A recent publication from this group concluded with the statement: “The generation of RNAs with chain lengths greater than 40 oligomers would have been long enough to initiate the first life on Earth”. Do natural clays catalyze this reaction? The attractiveness of this oligonucleotide synthesis rests in part on the ready availability of the catalyst. Montmorillonite 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 “catalytic activity of native montmorillonites is very poor. They interfere with phosphorylation reactions. The activity of the montmorillonite depended strongly on its physical source, with samples from Wyoming yielding the best results. Eventually the experimenters settled on Volclay, a commercially processed Wyoming montmorillonite provided by the American Colloid Company.

And now i will address the last claim: Namely self-replication. 



The RNA world is a hypothetical stage, in which self-replicating RNA molecules proliferated on the early earth. The term RNA world was coined by  American molecular biologist Walter Gilbert in 1986. The hope was, that evidence would be found demonstrating the ability of RNA to self-replicate. This would be the initial state of self-replication in a hypothetical origin-of-life scenario.  



An article in 2017 stated: Gilbert himself expressed some disappointment that after 30 years,  “a self-replicating RNA has not yet been synthesized or discovered” in the years since he predicted his hypothesis, but he remains optimistic that it will emerge eventually.



Many found the metaphor appealing: a world with a jack-of-all-trades RNA molecule, catalyzing the formation of indispensable cellular scaffolds, from which somehow then cells emerged. Others were quick to notice several difficulties with that scenario. These included the lack of templates enabling the polymerization of RNA in the prebiotic complex mixture and RNA’s extreme lability at moderate to high temperatures and susceptibility to base-catalyzed hydrolysis.

To go from a self-replicating RNA molecule to a self-replicating cell, which is in a literal sense a chemical factory, depending on at least the information stored in 500 thousand nucleotides, is a huge gap, that has not been addressed.  For a factory to make a duplicate, a copy of itself, it must employ and use a description of itself. This description, being a part of the original factory, must itself be prescribed by something else that is not itself. That is, it must come from the outside. Why?



In order to describe something, one needs to be a conscious agent, able to do so. If the factory itself was not the conscious agent, being able to observe itself, and describe itself, it must have been something else. I, as a human being, conscious as I am, can observe and describe myself. A non-conscious "something" has never been observed having these necessary cognitive and intellectual capabilities.



That's why the origin of biological information stored in genes is a hard, untractable problem for naturalists. It cannot be answered unless one acknowledges an intelligent designer.

The description of itself, in order to make a copy of itself, must be expressed. Parts, subunits, or an agglomeration of building blocks do not comprehend how they could shape themselves to move into the right functional form and position, become a subunit, and join to become part of a functional interlocked complex system. So in order to do so, and have the know-how to get energy directed precisely where needed to have the device performing and exercising its tasks, an organizing principle, and instructional assembly information to create such an irreducibly complex system must be there to direct the process and come from the outside. In the cell, this information is stored in genes. Unless that information directs the assembly and energy that moves the system away from equilibrium to perform its work, the individual parts would either lay around and remain unorderly, in a chaotic state, would remain non-assembled, disintegrate or, eventually, driven by random external forces, join into a basically infinite number of nonfunctional chaotic aggregational states.

Creating an interdependent system where the information, stored in hardware, is encoded, transmitted, and decoded to direct the assembly process of the identical representation of that digital information into an analog 3D form, the physical 'reality' of that description, adds untractable difficulty for unguided processes.



Furthermore, in order to have a copy, a daughter cell, identical to the mother cell, the description of itself must be passed to the offspring. Only then, a replica can be completed. The cause leading to a machine’s and factory's functionality and self-replication has only been found in the mind of intelligent engineers with foresight, intent, and goals, and nowhere else.



Memory-stored controls transform symbols into physical states. Von Neumann made no suggestion as to how these symbolic and material functions in life could have originated. He felt,

"That they should occur in the world at all is a miracle of the first magnitude."



To go from a bacterium to people is less of a step than to go from a mixture of amino acids to a bacterium.
[/size]

 James Compton
My name is James Compton, science researcher and book author. When talking about the origin of life, many believe that the issue is still a scientifically open question, that science is working towards solving the problem, and a solution near the next corner. Lee Cronin, for example, made a prediction in 2011. Unfortunately, it didn't concretize.  There are many reasons, why intelligent guidance had to be involved in the process. In this video, I will expose one reason. One of the most popular hypotheses is that life started with the so-called RNA world. Before we continue, a quick elucidation of what life is. As the shortest description, life is basically chemistry and information. More extendedly, life consists of Reproduction, Metabolism, Nutrition, Complexity, Organization,  Growth and development, storing and transmitting instructional complex Information, Hardware/software entanglement,   Permanence, and change. Donald Prothero wrote in his book: The evolving earth published in 2019: The simplest scenario for the origin of living, self-replicating systems would be an “RNA world.” The very first self-replicating form of life would be a single-stranded RNA, perhaps enclosed in a lipid bilayer membrane and perhaps using simple carbohydrates for food storage. Using both its replication powers and enzymatic powers, it would make more copies of itself and perform the role of the proteins as well until later, more complex reactions involving many different proteins could evolve. Every year, more discoveries are made that add details to our understanding of the origin of life and the RNA world. He starts his narrative with a single-stranded RNA. Here is the problem. In order for the RNA world to be true, one needs to start much earlier, namely with the origin of RNA itself. Only then, further questions can be asked, like how RNA polymerized, and eventually started self-replicating.  A number of reasons have been given why a prebiotic synthesis of RNA, and even more, DNA, is too complex. In cells, the synthesis of RNA and DNA requires extremely complex energy-demanding, finely adjusted, monitored,  and controlled anabolic pathways. Since they were not extant prebiotically, RNA had to be synthesized spontaneously on early earth by abiotic alternative non-enzymatic pathways.  This is one of the major, among many other unsolved origin of life problems. A recent article in the journal of the Royal Society claims that RNA, proteins and the genetic code that binds them each look like products of natural selection. I have no idea how they conclude that they seem the product of natural selection. To me, it indeed seems that these building blocks had to be selected, but nature has no intent, no goals, no aim to complexify molecules towards life. If a selection process was necessary, then it had to have another source, instead of nature. 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 nucleotides. In practice, the discrimination required to make nucleotide parts cleanly, or to assemble them correctly, seems insufficient.  Graham Cairns-Smith lists several hurdles that would have to be overcome.  


An article published in 2014 summarizes the current status quo: The first, and in some ways, the most important, problem facing the RNA World is the difficulty of prebiotic synthesis of RNA. This point has remained a focal point of the efforts of prebiotic chemists for decades. The ‘traditional’ thinking was that if one could assemble a ribose sugar, a nucleobase, and a phosphate, then a nucleotide could arise through the creation of a glycosidic bond and a phosphodiester bond. If nucleotides were then chemically activated in some form, then they could polymerize into an RNA chain. Each of these synthetic events poses tremendous hurdles for the prebiotic Earth, not to mention the often-invoked critique of the inherent instability of RNA in an aqueous solution. Thus, the issue arises of whether there could have been a single environment in which all these steps took place. Benner has eloquently noted that single-pot reactions of sufficient complexity lead to ‘asphaltization’ (basically, the production of intractable ‘goo’).


The asphalt problem has been outlined by Rob Stadler and Change Laura Tan in their book: Stairway to life



Even in a very short DNA of just two nucleotides, there are dozens of incorrect possible arrangements of the components, and only one correct arrangement. The probability of consistent arrangement decreases exponentially as the DNA lengthens. If natural processes could polymerize these monomers, the result would be chaotic “asphalt,” not highly organized, perfectly consistent biopolymers. Think about it — if monomers spontaneously polymerized within cells, the cell would die because all monomers would be combined into useless random arrangements.



And Steve Benner has made another observation, which means a death knell for the prebiotic synthesis or RNA: An enormous amount of empirical data has established, as a rule, that organic systems, given energy and left to themselves, devolve to give uselessly complex mixtures, “asphalts”. The literature reports (to our knowledge) exactly zero confirmed observations where evolution emerged spontaneously from a devolving chemical system. Further, chemical theories, including the second law of thermodynamics, bonding theory that describes the “space” accessible to sets of atoms, and structure theory requiring that replication systems occupy only tiny fractions of that space, suggest that it is impossible for any non-living chemical system to escape devolution to enter into the Darwinian world of the “living”. 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.


Another widespread myth is that RNA polymerization is something that has been demonstrated to be possible on clay. Robert Shapiro wrote a critique in regards to prebiotic proposals of clay-catalyzed oligonucleotide synthesis. An extensive series of studies on the polymerization of activated RNA monomers has been carried out by Ferris and his collaborators. A recent publication from this group concluded with the statement: “The generation of RNAs with chain lengths greater than 40 oligomers would have been long enough to initiate the first life on Earth”. Do natural clays catalyze this reaction? The attractiveness of this oligonucleotide synthesis rests in part on the ready availability of the catalyst. Montmorillonite 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 “catalytic activity of native montmorillonites is very poor. They interfere with phosphorylation reactions. The activity of the montmorillonite depended strongly on its physical source, with samples from Wyoming yielding the best results. Eventually the experimenters settled on Volclay, a commercially processed Wyoming montmorillonite provided by the American Colloid Company.

And now i will address the last claim: Namely self-replication. 


The RNA world is a hypothetical stage, in which self-replicating RNA molecules proliferated on the early earth. The term RNA world was coined by  American molecular biologist Walter Gilbert in 1986. The hope was, that evidence would be found demonstrating the ability of RNA to self-replicate. This would be the initial state of self-replication in a hypothetical origin-of-life scenario.  

An article in 2017 stated: Gilbert himself expressed some disappointment that after 30 years,  “a self-replicating RNA has not yet been synthesized or discovered” in the years since he predicted his hypothesis, but he remains optimistic that it will emerge eventually.

Many found the metaphor appealing: a world with a jack-of-all-trades RNA molecule, catalyzing the formation of indispensable cellular scaffolds, from which somehow then cells emerged. Others were quick to notice several difficulties with that scenario. These included the lack of templates enabling the polymerization of RNA in the prebiotic complex mixture and RNA’s extreme lability at moderate to high temperatures and susceptibility to base-catalyzed hydrolysis.

To go from a self-replicating RNA molecule to a self-replicating cell, which is in a literal sense a chemical factory, depending on at least the information stored in 500 thousand nucleotides, is a huge gap, that has not been addressed.  For a factory to make a duplicate, a copy of itself, it must employ and use a description of itself. This description, being a part of the original factory, must itself be prescribed by something else that is not itself. That is, it must come from the outside. Why?

In order to describe something, one needs to be a conscious agent, able to do so. If the factory itself was not the conscious agent, being able to observe itself, and describe itself, it must have been something else. I, as a human being, conscious as I am, can observe and describe myself. A non-conscious "something" has never been observed having these necessary cognitive and intellectual capabilities.

That's why the origin of biological information stored in genes is a hard, untractable problem for naturalists. It cannot be answered unless one acknowledges an intelligent designer.

The description of itself, in order to make a copy of itself, must be expressed. Parts, subunits, or an agglomeration of building blocks do not comprehend how they could shape themselves to move into the right functional form and position, become a subunit, and join to become part of a functional interlocked complex system. So in order to do so, and have the know-how to get energy directed precisely where needed to have the device performing and exercising its tasks, an organizing principle, and instructional assembly information to create such an irreducibly complex system must be there to direct the process and come from the outside. In the cell, this information is stored in genes. Unless that information directs the assembly and energy that moves the system away from equilibrium to perform its work, the individual parts would either lay around and remain unorderly, in a chaotic state, would remain non-assembled, disintegrate or, eventually, driven by random external forces, join into a basically infinite number of nonfunctional chaotic aggregational states.

Creating an interdependent system where the information, stored in hardware, is encoded, transmitted, and decoded to direct the assembly process of the identical representation of that digital information into an analog 3D form, the physical 'reality' of that description, adds untractable difficulty for unguided processes.

Furthermore, in order to have a copy, a daughter cell, identical to the mother cell, the description of itself must be passed to the offspring. Only then, a replica can be completed. The cause leading to a machine’s and factory's functionality and self-replication has only been found in the mind of intelligent engineers with foresight, intent, and goals, and nowhere else.

Memory-stored controls transform symbols into physical states. Von Neumann made no suggestion as to how these symbolic and material functions in life could have originated. He felt,

The origin of RNA is just a tiny problem compared to the huge number of things that have to be explained for life to start. If you want to know more, you can by the book: On the Origin of Life and Virus World by means of an Intelligent Designer: The Factory Maker, Paley's Watchmaker Argument 2.0, where not only the problem of the origin of RNA is addressed, but many other Origin of life issues. Thanks for watching, and please subscribe.

Graham Cairns-Smith 
So powerful has been the effect of Miller’s experiment on the scientific imagination that to read some of the literature on the origin of life (including many elementary texts) you might think that it had been well demonstrated that nucleotides were probable constituents of a primordial soup and hence that prevital nucleic acid replication was a plausible speculation based on the results of experiments. There have indeed been many interesting and detailed experiments in this area. But the importance of this work lies, to my mind, not in demonstrating how nucleotides could have formed on the primitive Earth, but in precisely the opposite: these experiments allow us to see, in much greater detail than would otherwise have been possible, just why prevital nucleic acids are highly implausible. Let us consider some of the difficulties to make RNA & DNA.
In Genetic Takeover I listed 14 major hurdles that would have to be overcome for primed nucleotides to have been made on the primitive Earth - from the build-up of sufficient and separate concentrations of formaldehyde and cyanide to the final 'winding-up' of the nucleotides. In practice each of these processes would be subdivided into separate unit operations that would have to be suitably sequenced. I think, to say that on average the 14 hurdles that I referred to in the making of primed nucleotides would each take 10 unit operations - that at least 140 little events would have to be appropriately sequenced. (If you doubt this, go and watch an organic chemist at work; look at all the things he actually does in bringing about what he would describe as 'one step' in an organic synthesis.) This is a huge number, represented approximately by a 1 followed by 109 zeros. This is the sort of number of trials that you would have to make to have a reasonable chance of hitting on the one outcome that represents success. Throwing one dice once a second for the period of the Earth's history would only let you get through about 10^15 trials.

Von Neumann: 

"That they should occur in the world at all is a miracle of the first magnitude."

Lynn margulis
To go from a bacterium to people is less of a step than to go from a mixture of amino acids to a bacterium.

The Deamer hypothesis proposes that the polymerization of RNA could have occurred in hot springs, such as those found in Yellowstone National Park. There are several challenges and limitations associated with this hypothesis:
Hot springs are characterized by high temperatures, which can be detrimental to the stability of RNA molecules. RNA is susceptible to degradation at elevated temperatures, and the RNA backbone can undergo hydrolysis, leading to the breakdown of the molecule. The ability of RNA to withstand and maintain its structural integrity in the extreme heat of hot springs is a significant challenge for the Deamer hypothesis. In hot spring environments, the high temperatures can promote reverse polymerization reactions, where RNA strands break down into individual nucleotides. This reverse reaction hampers the accumulation and maintenance of longer RNA chains necessary for the development of functional RNA molecules. Hot springs often have high water flow rates, resulting in dilute solutions. The low concentrations of necessary reactants, such as nucleotides, in such environments can impede the efficient polymerization of RNA molecules. Adequate concentrations of nucleotides are required for the successful formation and elongation of RNA chains. Hot springs contain various minerals and metal ions that can interact with nucleotides and RNA molecules, potentially inhibiting or interfering with their polymerization processes. These chemical interactions may lead to the formation of stable complexes or hinder the stability and functionality of RNA. While the Deamer hypothesis provides a mechanism for the emergence of RNA in hot springs, direct experimental evidence supporting this specific scenario is limited. Conducting experiments in hot spring-like conditions to demonstrate the polymerization of RNA and its stability under such extreme conditions is challenging.