Rosa Rubicondior: Abiogenesis News - Not Random Chance Or Divine Magic But Natural Selection

The sugar ribose is more quickly phosphorylated compared to other sugars with the same chemical formula but a different shape. This selective phosphorylation could explain how ribose became the sugar molecule in RNA.

Credit: Scripps Research

Where did RNA come from? | Scripps Research

One fallacy with which anyone who has tried to engage a creationist in debate will soon become familiar is the false dichotomy. This is where a creationist attempts to make a "god of the gaps" argument appear logical by presenting it as a binary choice between something so simplistic or absurd that no serious scientist would argue for it—and "God did it!" In doing so, they ignore the actual scientific explanations and exclude all other plausible natural mechanisms.

A classic example of this is the argument that abiogenesis—often deliberately misrepresented as the spontaneous assembly of a complex, living cell from inorganic materials—is far too improbable to have occurred by chance alone, and therefore must have required a supernatural intelligence. In their minds, the very existence of complex life is "proof" of their particular deity.

This line of reasoning overlooks the crucial role played by natural processes, such as chemistry and physics, and what amounts to an evolutionary process at the molecular level. In such a process, chemical pathways that are more efficient at producing copies of themselves are naturally favoured, leading over time to increased refinement and complexity. For instance, why was the five-carbon sugar ribose selected as the backbone sugar in RNA?

This is the question that two researchers at the Scripps Research Institute have tackled. They demonstrated that ribose is far more efficiently phosphorylated than its alternatives, forming the chemical basis of nucleotides—the building blocks of RNA (and later DNA). This efficiency gave ribose a natural advantage, allowing it to "win" the competition against other sugars.

Their findings show that the emergence of ribose was not the result of random chance, but the predictable outcome of the underlying chemistry and physics. The study has been published in the international edition of the journal of the German Chemical Society, Angewandte Chemie.

The work is also summarised in accessible terms in a Scripps Research press release.

In summary, what the research shows is prebiotic evolution at the chemical level: Key Technical Findings

Selective phosphorylation of ribose by diamidophosphate (DAP)
The team investigated how ribose—compared with three structural isomers (arabinose, lyxose, and xylose)—reacts with a prebiotic phosphorylating agent, diamidophosphate (DAP). They discovered thatribose undergoes phosphorylation far more rapidly and efficiently, swiftly converting into ribofuranose‑1,2‑ and 2,3‑cyclic phosphates. In contrast, the other sugars formed DAP‑adducts much more slowly, and only eventually yielded cyclic products [1].

Ribofuranose specificity emerges naturally
This reaction showcases a natural chemical “selection” for the ribofuranose structure, which is the form used in RNA. When ribose was reacted as part of a pentose mixture, theribofuranose-1,2-cyclic phosphate predominated, indicating that ribose has an inherent chemical advantage over its isomers in prebiotic phosphorylation [2].

Mechanistic confirmation via NMR spectroscopy
Using nuclear magnetic resonance (NMR) spectroscopy, the researchers confirmed not only the speed and extent of phosphorylation, but also the structural identity of the products—showing clearly that ribose forms cyclic phosphate linkages more readily than its isomers [3].

Implications for the RNA-world hypothesis
Because ribose couples quickly and firmly with phosphate—a key step in nucleotide formation—its dominance in early chemistry would have enabled the consistent formation of ribonucleotides under plausible prebiotic conditions. This supports the notion that ribose's centrality in RNA wasn’t due to random chance, but a deterministic outcome of chemistry and physics [1].

Why this matters

Chemical determinism: Demonstrates ribose would naturally outcompete similar sugars based on reactivity, not luck.
Acceleration of prebiotic pathways: Quick phosphorylation by DAP points to possible pathways toward RNA nucleotides before enzymes existed.
Supports RNA-first models: Provides experimental grounding for the RNA-world hypothesis by explaining ribose's emergence.

Broader Context

This fits into a growing body of research showing how prebiotic chemistry could have steered complex biomolecules like nucleotides — even before life began. Similar approaches, like Eschenmoser’s phosphorylated formose chemistry, also point to chemical selection as a driver of early molecular evolution [3, 4, 5, 6].

In short: the study reveals that ribose wasn't picked by chance — it was chemically inevitable, thanks to its rapid, efficient phosphorylation into cyclic phosphates. This gives powerful evidence that the building blocks of life emerged through natural chemical logic, not divine intervention.

Where did RNA come from?
Origin-of-life scientists from Scripps Research reveal how the sugar ribose may have been selected as one of life’s building blocks.
In living organisms today, complex molecules like RNA and DNA are constructed with the help of enzymes. So how did these molecules form before life (and enzymes) existed? Why did some molecules end up as the building blocks of life and not others? A new study by Scripps Research scientists helps answer these longstanding questions.

The results, published in the chemistry journal Angewandte Chemie on June 27, 2025, show how ribose may have become the sugar of choice for RNA development. They found that ribose binds to phosphate—another molecular component of RNA—more quickly and effectively than other sugar molecules. This feature could have helped select ribose for inclusion in the molecules of life.

This gives credence to the idea that this type of prebiotic chemistry could have produced the building blocks of RNA, which then could have led to entities which exhibit lifelike properties.

Professor Ramanarayanan Krishnamurthy, corresponding author
Department of Chemistry
The Scripps Research Institute
La Jolla, CA, USA
Nucleotides, the building blocks of RNA and DNA, consist of a five-carbon sugar molecule (ribose or deoxyribose) that is bound to a phosphate group and a nitrogen-based base (the part of the molecule that encodes information, e.g., A, C, G or U). Krishnamurthy’s research aims to understand how these complex molecules could have arisen on primordial Earth. Specifically, this study focused on phosphorylation, the step within nucleotide-building where ribose connects to the phosphate group.

Phosphorylation is one of the basic chemistries of life; it’s essential for structure, function and metabolism. We wanted to know, could phosphorylation also play a fundamental role in the primordial process that got all of these things started?

Professor Ramanarayanan Krishnamurthy

From previous work, the team knew that ribose could become phosphorylated when combined with a phosphate-donating molecule called diamidophosphate (DAP). In this study, they wanted to know whether other, similar sugars could also undergo this reaction, or whether there is something special about ribose.

To test this, the researchers used controlled chemical reactions to investigate how quickly and effectively ribose is phosphorylated by DAP compared to three other sugar molecules with the same chemical makeup but a different shape (arabinose, lyxose and xylose). Then, they used an analytical technique called nuclear magnetic resonance (NMR) spectroscopy to characterize the molecules produced by each reaction.

They showed that although DAP was able to phosphorylate all four sugars, it phosphorylated ribose at a much faster rate. Additionally, the reaction with ribose resulted exclusively in ring-shaped structures with five corners (e.g., 5-member rings), whereas the other sugars formed a combination of 5- and 6-member rings.

This really showed us that there is a difference between ribose and the three other sugars. Ribose not only reacts faster than the other sugars, it's also more selective for the five-member ring form, which happens to be the form that we see in RNA and DNA today.

Professor Ramanarayanan Krishnamurthy

When they added DAP to a solution containing equal amounts of the four different sugars, it preferentially phosphorylated ribose. And whereas the other three sugars got “stuck” at an intermediate point in the reaction, a large proportion of the ribose molecules were converted into a form that could likely react with a nuclear base to form a nucleotide.

What we got was a 2-in-1: We showed that ribose is selectively phosphorylated from a mixture of sugars, and we also showed that this selective process produces a molecule with a form that is conducive for making RNA. That was a bonus. We did not anticipate that the reaction would pause at the stage advantageous for producing nucleotides.

Professor Ramanarayanan Krishnamurthy

The researchers caution that, even if these reactions can all occur abiotically, it doesn’t mean that they are the reactions that necessarily resulted in life.

Studying these types of chemistries helps us understand what sort of processes might have led to the molecules that constitute life today, but we are not making the claim that this selection is what led to RNA and DNA, because that’s quite a leap. There are a lot of other things that need to happen before you get to RNA, but this is a good start. The next question is, can ribose be selectively enriched within a protocell, and can it further react to make nucleotides within a protocell? If we can make that happen, it might produce enough tension to force the protocell to grow and divide — which is exactly what underpins how we grow.

Professor Ramanarayanan Krishnamurthy

In future research, the team plans to test whether this chemical reaction can occur inside primitive cellular structures called “protocells.”

In addition to Krishnamurthy, the study “Selection of Ribofuranose-Isomer Among Pentoses by Phosphorylation with Diamidophosphate” was co-authored by Harold A. Cruz of Scripps Research.

Publication:
H. A. Cruz, R. Krishnamurthy, Angew.
Selection of Ribofuranose-Isomer Among Pentoses by Phosphorylation with Diamidophosphate
Chem. Int. Ed. 2025, e202509810. https://doi.org/10.1002/anie.202509810.

Graphical Abstract
Diamidophosphate phosphorylates the four pentoses under mild aqueous conditions. Ribofuranosyl-cyclicphosphates are formed efficiently, while the other three pentoses react slowly to form furanosyl- and/or pyranosyl-forms. The selective formation of ribofuranosyl-1,2-cyclicphosphate occurs even when starting from a mixture of sugars suggesting an alternative pathway for abiotic synthesis of ribonucleotides in a prebiotic context.

Abstract
The unique structure–function relationship of the ribofuranose ring in RNA has inspired various chemical pathways to select for the ribofuranose form (over the ribopyranose form), especially in a prebiotic context. Herein we show that the reaction of diamidophosphate (DAP) with the four pentoses—ribose, arabinose, xylose, and lyxose—naturally selects the ribofuranose form more efficiently when compared to the other three pentoses. All four pentoses form the initial diamidophosphate-adduct; however, ribose undergoes rapid conversion to ribofuranose-1,2- and 2,3-cyclicphosphate products, while the other three pentoses show significant accumulation of the initially formed DAP-adducts and slow conversion to the cyclicphosphate products. Arabinose and xylose show a distribution between furanose- and pyranose-1,2-cyclicphosphate products, while lyxose forms the furanose-1,2- and pyranose-2,3-cyclicphosphate products. This trend is also manifested when starting from a mixture of pentoses where ribofuranose 1,2-amidocyclicphosphate dominates the product distribution. Such selection for ribofuranose among pentoses by phosphorylation i) provides another venue of how a ribofuranose structure can selectively emerge through abiotic chemical reaction suitable for elaboration toward RNA and ii) adds to the body of experimental work addressing the chemical origin of RNA.

H. A. Cruz, R. Krishnamurthy, Angew.
Selection of Ribofuranose-Isomer Among Pentoses by Phosphorylation with Diamidophosphate
Chem. Int. Ed. 2025, e202509810. https://doi.org/10.1002/anie.202509810.

© 2025 John Wiley & Sons, Inc.
Reprinted under the terms of s60 of the Copyright, Designs and Patents Act 1988.

This research delivers yet another blow to the creationist argument that the origin of life is too improbable to have happened without supernatural intervention. Far from being a random or miraculous event, the emergence of life's basic building blocks — such as RNA — can now be shown to follow predictable chemical pathways under plausible prebiotic conditions. The efficient phosphorylation of ribose demonstrates that molecular selection was at work even before biological evolution began, with chemistry and physics favouring molecules that could form the basis of replication and inheritance.

What this study reinforces is that complexity can arise not in spite of natural law, but because of it. Molecules that were more reactive and more stable in forming key intermediates — such as ribose forming cyclic phosphates — would have naturally accumulated and outcompeted less favourable alternatives. This is not a process of blind luck, but one of natural filtering, where favourable outcomes are preserved and reinforced by their inherent chemical advantages. It's an analogue to Darwinian selection, operating at the level of molecules rather than organisms.

Creationist claims often rest on a profound misunderstanding — or misrepresentation — of how probability and natural processes interact. By ignoring the fact that nature selects and amplifies the most efficient outcomes, they present a straw man version of abiogenesis as a single, sudden leap from inert matter to fully formed life. But studies like this show that life need not have emerged through an implausible series of coincidences. Instead, it arose through a stepwise progression governed by the deterministic logic of chemistry, in which some molecules—like ribose—won the chemical ‘race’ simply because they were best suited to the task.

In this light, the creationist assertion that life is too complex to have arisen naturally is not just scientifically baseless; it is an admission of ignorance about the richness and subtlety of natural processes. As our understanding of prebiotic chemistry deepens, the gap in which a supernatural designer might have been hiding grows ever smaller — and less necessary.

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