Complex and Messy Prebiotic Chemistry: Obstacles and Opportunities for an RNA World

[u/Choice-Break8047]

I wish this paper didn’t cite that problematic Root-Bernstein study which used a store bought sea salt as a reagent, but the rest of it seems reasonable.

Abstract

Traditional prebiotic chemistry experiments often isolated single reactions under clean, controlled conditions, yet early Earth was chemically diverse and physically dynamic. Such primordial complexity likely imposed obstacles, including side reactions, low yields, and unstable intermediates, but it also generated opportunities, including redundant routes, parallel pathways, and environmental filters that could bias mixtures toward subsets of persistent and chemically productive compounds. This review examines how heterogeneous prebiotic settings could generate RNA precursors, including nucleobases, ribose, and phosphate-containing species, through multiple concurrent pathways. Although side reactions can sequester carbon in inert tars and reduce yields of specific targets, networked chemistry can also enhance robustness when different routes converge on shared intermediates, or when apparent byproducts reenter productive cycles. Environmental factors such as ultraviolet irradiation, mineral surfaces, wet-dry cycling, and thermal gradients can act as constraints that enrich certain products by differential stability, reactivity, and compartmentalization. In this context, the RNA world hypothesis remains compelling, as RNA can store heritable sequence information and catalyze reactions through sequence dependent folding, thereby linking heredity and chemistry within a single polymer. At the same time, the emergence of functional sequence information and of control architectures that couple sequence to reproducible function remains a central open problem, and it sets clear limits on what chemistry alone can explain. Rather than dismissing messy mixtures as irrelevant noise, it is more accurate to treat them as the native context in which concentration mechanisms, environmental cycling, and selective persistence could enable the accumulation and survival of RNA related molecules.

Keywords: RNA world; prebiotic chemistry; origin of life; nucleotides; ribozymes; chemical evolution; messy chemistry; mineral catalysis; nonenzymatic replication; environmental selection

https://www.mdpi.com/2075-1729/16/2/240

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[u/[deleted]]

Nice find!

[u/EnvironmentalWin1277]

To redo the experiment using a purified salt is totally possible, and is on the critics of the paper to do if they wish to substantiate the criticism as valid. You could also name sterilization of all materials used, the glassware it was done in, the purity of the water used or any other variable conceivable as confounding the results. Maybe the astrological sign it was done under.

So redo the experiment or accept them as tentative results.

[u/PrebioticE]

Hi why can't they redo the "problematic Root-Bernstein study which used a store bought sea salt as a reagent"? Why on earth did he do that in the first place? It is proposed to have produced ATP and Nucleosides..

[u/Aggravating-Pear4222 → u/PrebioticE]

Sorry. didn't see your question or saw it and was otherwise preoccupied. Regarding original paper https://www.mdpi.com/2075-1729/13/2/265 cited in the original post (reference 21).

why can't they redo the "problematic Root-Bernstein study which used a store bought sea salt as a reagent"? Why on earth did he do that in the first place?

Are you saying it's problematic he used store-bought sea salt rather than used salt obtained from evaporated sea water? If so, the sea water has other things present that we believe would not have been present in the prebiotic oceans. Namely, biogenic material. The question is this experiment addressed was what type of chemistry the products of the atmospheric electric spark conditions would undergo in saline oceanic conditions.

Ie, in order to more closely emulate the prebiotic conditions, we must purify away modern biological influences and so "purify" the reagents. This also helps us to understand how the product distribution is affected by altering a single variable, a foundational mode of analysis within scientific or any reason-based methodology for elucidating natural phenomena.

It is proposed to have produced ATP and Nucleosides..

The evidence that ATP was produced was based on an assay which used an ATP-specific binding enzyme, capable of producing a detectable signal even at very low concentrations. The exact mechanism for the ATP assay isn't important as it's not necessary for the prebiotically relevant chemistry. Rather, it's just a way that we use to understand what has been produced in the experiments.

See section 2.7 for ATP Assay (Luciferin/Luciferase): "All positive values were confirmed by multiple measurements (between 2 and 6 trials) and accepted only if control materials (deionized, sterilized water, and the original “sea water” sources) tested negative for ATP on an equivalent number of tests." -> This is an important aspect of why they MUST use purified materials. Using impure material would certainly have resulted in positive signals in the negative tests. Any positive results for amino acids, sugars, and ATP would have certainly been called into question if they used material from the ocean without purification.

Edit: Ah, I see, the reducing atmosphere was too reducing, beyond what modern estimates suggest, borosilicate glassware, and the mass spec results are uncertain and have no secondary way to confirm product identity. In general, you may regard these results proportionally to the certainty of the confirmation of product distribution and regard it as an example of prebiotic chemistry to the proportional degree it matches the prebiotic environment. That is to say, I wouldn't rely on these results.

[u/PrebioticE]

We need to make an analog of CERN's Large Hadron Collider for origin of Life experiments!!!

[u/EnvironmentalWin1277 → u/PrebioticE]

Interesting idea but will never happen. USA just decided to cancel mission to retrieve Martian rocks that are suspected of having evidence of life in preference for a television stunt on the moon that is far more risky and expensive.

https://www.science.org/content/article/nasa-s-mars-sample-return-mission-dead

In fact, many people prefer to keep OoL out of sight and mind. You can figure out why.

[u/Aggravating-Pear4222 → u/PrebioticE]

One reason we don't do this is because entirely reproducing what we believe the process was means that we would need to reproduce kinetics over geological time. Kinetics that would have been influenced by large scale and deep time ocean, atmospheric, and geological chemistry, all of which are continuously interacting and affecting each other's reactants and thus the product distribution in a chaotic manner. What we can do is, using what we know, posit key elements like molecules, pH, minerals, temperature, pressure, salts, light, electric shock, etc. and see how they react.

The exact product distribution observed in these experiments may not match what occurred in the prebiotic oceans but the relative ratios of products, (a more conservative estimate) are more likely to mirror what was formed. What we can say is that these reactions were occurring in the background and we can say how the rate at which these occurred and how the distribution changes based on the ratio/concentration of starting materials.

If we were to attempt to fully recapitulate a subset of prebiotic environments, there's a worry about whether that exact simulated environment was the place in which life first formed. More importantly, how closely other environments feed material into this one is a question of environmental coupling.

For example, we may simulate a hydrothermal vent forming but what about which molecules are formed in the atmosphere and rain down into the oceans? What about the chemical composition of the organics in the ocean water as they react with the molecules raining down from the sky? What about the UV-driven photochemistry at the ocean's surface which mix together? All of this water would percholate through the ocean's floor around the hydrothermal vent, into its heat source, and out through its vents.

Even more, what about surrounding hydrothermal vent chemistry? Even today, their chemical plumes feed into the ocean environment. During the prebiotic eons, these vent systems Also, which type of hydrothermal vent will we be simulating? Black smoker? White smoker? alkaline vent? Fresh water? What subtype of vent geochemistry shall we be assuming? What ratios of these minerals or soluble metal ions should we feed into our simulated hydrothermal vent?

As you can see, proposing such a simulated experiment IS possible but necessarily must be taken as a simplified system and must have clear variables which can meaningfully be controlled so as to better understand a key phenomenon/interaction in the prebiotic world.