Prebiotic Chemistry and Formation of Basic Building Blocks

I. Prebiotic Chemistry and Formation of Basic Building Blocks

This stage would have presented significant challenges in forming life's basic molecular building blocks—amino acids, nucleotides, sugars, and lipids—under early Earth conditions. The random nature of chemical reactions and the specific conditions required for these molecules to assemble would have made their spontaneous formation highly improbable, representing a massive hurdle in the origin of life.

1. Prebiotic Chemistry

The chemical synthesis of organic compounds in the prebiotic world is a cornerstone of the origin of life research, offering insights into how the building blocks of life may have formed before the emergence of biological systems. This exploration into prebiotic chemistry delves into the various organic molecules, reactions, and processes believed to have been pivotal in Earth's early history. The prebiotic era is said to have begun with simple organic molecules present in the primordial atmosphere and oceans. Compounds such as formaldehyde, hydrogen cyanide, and ammonia would have served as fundamental precursors for more complex biomolecules. From these humble beginnings, a cascade of chemical reactions would have given rise to the diverse array of organic compounds necessary for life. As we examine the prebiotic synthesis of increasingly complex molecules - amino acids, nucleobases, sugars, and lipid precursors - we begin to see the chemical foundations of life taking shape. Each of these molecular classes plays an indispensable role in modern biological systems, and understanding their abiotic formation is crucial for hypothesizing life's emergence. Key reactions and processes that could have facilitated the formation of these organic compounds span a range of potential prebiotic environments. From atmospheric processes modeled in the famous Miller-Urey experiment to reactions in hydrothermal vents and on mineral surfaces, the possible settings for prebiotic chemistry are diverse. Beyond mere synthesis, other critical aspects of prebiotic chemistry demand attention. Concentration mechanisms that would have accumulated dilute organic compounds into more reaction-favorable conditions are essential to consider. Additionally, the emergence of chirality - a defining feature of biological molecules - presents a considerable puzzle with various proposed solutions. While our understanding of prebiotic organic synthesis has advanced significantly, many aspects remain unsolved. The field continues to evolve as new experimental techniques are developed and our knowledge of early Earth conditions improves. By examining these potential prebiotic syntheses and processes, we gain valuable insight into the chemical foundations that would have preceded and enabled the origin of life. This exploration sets the stage for understanding how more complex biomolecules, including the first enzymes and proteins, would have emerged in the journey towards the supposed  Last Universal Common Ancestor (LUCA) and the remarkable diversity of life we observe today.

1.1. Chemical synthesis of organic compounds

In the early 19th century, a distinction emerged between substances derived from living organisms and those from non-living sources. This divide gave birth to the concept of "vitalism," positing that organic compounds possessed a unique "vital force" exclusive to living entities. The year 1828 marked a turning point when Friedrich Wöhler successfully synthesized urea from inorganic precursors. This groundbreaking achievement challenged the prevailing vitalism theory, prompting a reevaluation of the organic-inorganic dichotomy. Gradually, the definition of organic compounds shifted from their origin to their chemical composition. In modern chemistry, organic compounds are primarily defined by the presence of carbon atoms in their structure. This broader definition encompasses a wide spectrum of substances, from those indispensable for biological processes to synthetic materials never found in nature. Notable exceptions include carbon dioxide and carbonates, which remain classified as inorganic despite containing carbon.

When examining the list of compounds provided:

- Formaldehyde (CH2O), hydrogen cyanide (HCN), and methane (CH4) fall within the organic category due to their carbon-hydrogen bonds.
- Ammonia (NH3), carbon dioxide (CO2), and water (H2O) are technically inorganic. However, their role in prebiotic chemistry and life's origins often places them in discussions alongside organic compounds.

These simple molecules play an essential role in the formation of more complex organic structures necessary for life. Their reactive nature and combinatorial potential make them fundamental components in theories exploring life's origins and in contemporary biochemistry.

1.2. Simple organic molecules

1. Formaldehyde (CH2O): A key precursor for more complex organic molecules, including sugars through the formose reaction.
2. Hydrogen cyanide (HCN): Important for the synthesis of amino acids and nucleobases.
3. Ammonia (NH3): A source of nitrogen for amino acids and other biologically important molecules.
4. Methane (CH4): Can serve as a carbon source and participate in various organic reactions.
5. Carbon dioxide (CO2): A carbon source for various organic compounds and important for early metabolic processes.
6. Water (H2O): The universal solvent, crucial for all known life processes.

These molecules are considered "building blocks" of life, as they can react and combine to form more complex organic compounds essential for living systems, such as amino acids, nucleotides, and sugars.

1.2.1. The Role and Challenges of Key Prebiotic Molecules in the Origin of Life

Formaldehyde (CH₂O)

Formaldehyde is a simple organic molecule that serves as a key precursor for more complex organic compounds, including sugars through the formose reaction. The formose reaction involves the condensation of formaldehyde molecules to form sugars like ribose, which are essential components of nucleic acids such as RNA and DNA. However, the availability and stability of formaldehyde on the prebiotic Earth present significant challenges. Formaldehyde is highly reactive and tends to polymerize spontaneously, reducing its availability for critical prebiotic reactions. Additionally, the synthesis of formaldehyde requires specific conditions, such as ultraviolet irradiation of methane and carbon monoxide mixtures, which may not have been consistently present on the early Earth. Moreover, the formose reaction itself is highly sensitive to environmental conditions, including pH, temperature, and the presence of catalytic minerals. Without precise conditions, the reaction yields a complex mixture of sugars and tar-like substances, making the selective synthesis of biologically relevant sugars improbable under natural settings.

Hydrogen Cyanide (HCN)

Hydrogen cyanide is another crucial molecule in prebiotic chemistry, important for the synthesis of amino acids and nucleobases. HCN can react with itself and other molecules to form adenine, one of the nucleobases in RNA and DNA, and amino acids like glycine and alanine. The formation of HCN on the prebiotic Earth likely required a reducing atmosphere rich in methane and nitrogen, with energy inputs like ultraviolet light or electric discharges (lightning). However, geological evidence suggests that the early Earth's atmosphere may not have been sufficiently reducing to favor HCN production in significant amounts. Furthermore, HCN is highly toxic and volatile, raising questions about its accumulation and concentration in prebiotic environments. Its reactivity also means it can polymerize into inert compounds, reducing its availability for the synthesis of biologically important molecules.

The Challenges of Obtaining Ammonia on the Prebiotic Earth

The spontaneous formation of ammonia (NH₃) on the prebiotic Earth presents significant challenges for naturalistic explanations of the origin of life. Nitrogen is an essential component of amino acids, nucleotides, and other biomolecules vital for life. However, atmospheric nitrogen exists predominantly as diatomic nitrogen gas (N₂), a molecule characterized by a strong triple bond (N≡N) that makes it remarkably inert and unreactive under standard conditions. In modern biological systems, certain microorganisms possess the enzyme nitrogenase, which can reduce atmospheric N₂ to ammonia through a process known as nitrogen fixation. This enzyme is a complex metalloprotein containing iron and molybdenum cofactors, enabling the cleavage of the triple bond under ambient temperatures and pressures. The reaction requires significant energy input, supplied by ATP, highlighting the sophisticated nature of this biological process. On the prebiotic Earth, such enzymatic mechanisms were not available. The question then arises: how could ammonia have formed naturally to supply the necessary reduced nitrogen for the synthesis of amino acids and nucleotides? One hypothesis suggests that abiotic processes, such as lightning strikes or high-energy events, could have provided the necessary energy to fix nitrogen. Lightning can produce enough energy to break the N≡N bond, leading to the formation of reactive nitrogen species like nitric oxide (NO) and nitrogen dioxide (NO₂). However, these are oxidized forms of nitrogen and would require further reduction to form ammonia—a process not favorable without enzymatic assistance. Another proposed mechanism involves the reduction of nitrogen gas via mineral catalysts present on the early Earth. Certain minerals, such as iron-sulfur compounds found near hydrothermal vents, might have facilitated the conversion of N₂ to NH₃ under high-temperature and high-pressure conditions. While laboratory experiments have shown some potential for such reactions, the efficiency and yield are generally low, casting doubt on whether sufficient amounts of ammonia could be produced through this route.

Methane (CH₄)

Methane can serve as a carbon source and participate in various organic reactions crucial for the origin of life. In prebiotic chemistry, methane is considered a key component in the synthesis of more complex organic molecules when subjected to energy sources like ultraviolet radiation or electrical discharges. One challenge with methane is its abundance and stability in the early Earth's atmosphere. Significant concentrations of methane require a strongly reducing environment, which is a matter of debate among scientists studying the early atmosphere. If the atmosphere was more neutral or oxidizing, methane levels would have been low, limiting its role in prebiotic synthesis pathways. Additionally, methane is relatively inert under standard conditions, meaning substantial energy input is required to activate it for further reactions. The efficiency of such activation processes under prebiotic conditions remains uncertain.

The Challenges of Carbon Fixation on the Prebiotic Earth

Carbon is another fundamental element in biological molecules, serving as the backbone for organic compounds. On the prebiotic Earth, the primary source of carbon was atmospheric carbon dioxide (CO₂), a stable and oxidized molecule. Converting CO₂ into reduced, organic forms requires substantial energy input and specialized catalytic processes. In contemporary organisms, carbon fixation is achieved through several complex biochemical pathways, such as the Calvin-Benson cycle, the reductive citric acid cycle, and the Wood-Ljungdahl pathway. These pathways utilize sophisticated enzymes and coenzymes to reduce CO₂ and incorporate it into organic molecules. For instance, the enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) plays a critical role in the Calvin-Benson cycle by catalyzing the fixation of CO₂ into a usable organic form. In the absence of these biological mechanisms, the prebiotic fixation of carbon presents a significant obstacle. Abiotic pathways for reducing CO₂ under prebiotic conditions are limited and typically inefficient. Some theories propose that metal catalysts, like those containing nickel or iron, could facilitate the reduction of CO₂ in hydrothermal vent environments. Reactions such as the Fischer-Tropsch type synthesis have been considered, where CO₂ and hydrogen gas react over metal surfaces to form hydrocarbons. However, these reactions often require specific conditions and yield a mixture of products, many of which are not directly relevant to biological systems. Moreover, the concentrations of reactants and the environmental conditions necessary for these abiotic reactions would have been highly variable on the early Earth. The dilution of key molecules in the vast oceans further reduces the likelihood of sufficient organic carbon production through these means.

Water (H₂O)

Water is the universal solvent and is crucial for all known life processes. It provides the medium in which biochemical reactions occur and influences the structure and function of biomolecules. Paradoxically, while water is essential for life, it also poses challenges for prebiotic chemistry. Many of the polymerization reactions required to form proteins and nucleic acids are dehydration synthesis reactions, which involve the removal of a water molecule. In an aqueous environment, these reactions are thermodynamically unfavorable, as water tends to hydrolyze bonds rather than form them. This "water paradox" presents a significant hurdle in origin-of-life scenarios. Various hypotheses have been proposed to overcome this challenge, such as the presence of drying cycles in tidal pools, mineral surfaces that concentrate reactants and facilitate dehydration reactions, or alternative solvents in localized environments.


Open Questions in Prebiotic Organic Molecule Formation

1. Source and Concentration of Precursor Molecules:
Origin and accumulation of simple organic molecules on early Earth unclear. Challenges: uncertain early atmosphere composition complicates modeling; higher reactant concentrations are needed than believed possible in primordial oceans. No known mechanisms explain organic molecule concentration or preservation of reactive species.
2. Polymerization in Aqueous Environments:
Formation of biopolymers in water faces thermodynamic challenges. Water promotes hydrolysis, breaking down polymers. Unknown energy sources for unfavorable polymerization reactions. Difficult to explain without specialized enzymes or guided processes.
3. Selective Formation of Biologically Relevant Molecules:
Prebiotic reactions yield many non-biological compounds. Unclear how biologically relevant molecules were preferentially formed/selected. Abiotic reactions lack preference for useful molecules. Challenging to explain exclusion of irrelevant/harmful compounds in prebiotic environment.
4. Coordination of Multiple Prebiotic Processes:
Simultaneous emergence of complex biomolecules (proteins, nucleic acids, lipids) is problematic. Many processes require multiple interacting parts (e.g., genetic code, enzymes, translation machinery). No clear pathway for the stepwise emergence of interdependent systems.
5. Preservation and Accumulation of Organic Compounds:
Stability of organics in harsh early Earth conditions unresolved. Challenges: intense UV radiation, and geological activity (volcanoes, meteor impacts). How organic molecules survived and accumulated remains unexplained.
6. Information Content and Self-Replication:
Origin of self-replicating molecules and genetic code highly challenging. Unknown: how specific codon-amino acid associations arose, nature of first self-replicator. No known mechanism for spontaneous generation of complex, specified information needed for self-replication. Genetic code origin remains a major mystery.

These unresolved questions illustrate the significant challenges scientists face when trying to explain the origin of essential organic molecules through purely naturalistic processes. Each issue highlights conceptual problems that current models struggle to address adequately, pointing to the need for further research and potentially new paradigms in understanding prebiotic chemistry and the origin of life.

1.3. Origin of the organic compounds on the prebiotic earth

The question of the origin of organic compounds on early Earth is fundamental in origin-of-life research. This topic was first tackled in-depth by Stanley Miller and Harold Urey in 1953, who simulated early Earth conditions in the lab to study the synthesis of amino acids. Their work was based on the hypothesis that Earth’s primitive atmosphere was reducing and conducive to organic synthesis. In a 1959 study, Miller and Urey revisited these concepts:

"Oparin further proposed that the atmosphere was reducing in character and that organic compounds might be synthesized under these conditions. This hypothesis implied that the first organisms were heterotrophic—that is, that they obtained their basic constituents from the environment instead of synthesizing them from carbon dioxide and water. Various sources of energy acting on carbon dioxide and water failed to give reduced carbon compounds except when contaminating reducing agents were present. The one exception to this was the synthesis of formic acid and formaldehyde in very small yields by the use of 40-million-electron volt helium ions from a 60-inch cyclotron. While the simplest organic compounds were synthesized, the yields were so small that this experiment can be best interpreted to mean that it would not have been possible to synthesize compounds nonbiologically as long as oxidizing conditions were present on the Earth." 1

Despite these pioneering efforts, the issue of how organic compounds originated on Earth remains unsolved and debated today. In 2022, a science report claimed:
"Likely energy source behind first life on Earth found ‘hiding in plain sight.’" 2 This suggests that even after 67 years since Miller's first investigation, the question is still open. Researchers like Jessica Wimmer and Professor William Martin proposed that life could have emerged at hydrothermal vents:
"The new findings uncover a natural tendency of metabolism to unfold under the environmental conditions of H2-producing submarine hydrothermal vents. No light or other source of radiation was required. Just H2 and CO2 in the dark. Our calculations indicate whether a reaction can go forward. Whether or not reactions will go forward depends on the presence of catalysts, which are abundant at H2-producing hydrothermal vents."

However, these researchers presuppose that the 400 reactions they reference were already extant, raising the question: how can we know that non-enzymatic reactions replaced enzymatic ones in early Earth conditions? Leslie Orgel, a prominent figure in origin-of-life research, had already voiced skepticism about such speculative hypotheses in 2008 3.

1.3.1. Origin of the Proteinogenic Amino Acids Used in Life

There are many hypotheses about how the amino acids used in life originated, ranging from terrestrial to extraterrestrial proposals. Terrestrial origins include spark discharge, irradiation (UV, X-ray), shock heating, and hydrothermal vents. Extraterrestrial amino acids, on the other hand, have been found in carbonaceous chondrites, comets, and micrometeorites. Norio Kitadai and colleagues provided a comprehensive overview of these possibilities in their 2017 review: "To date, over 80 kinds of amino acids have been identified in carbonaceous chondrites, including 12 protein-amino acids such as Ala, Asp, Glu, Gly, Ile, Leu, Phe, Pro, Ser, Thr, Tyr, and Val." 4

Despite these discoveries, one major issue is that these amino acids are always found in mixtures with non-proteinogenic amino acids, and they exist as racemic mixtures (i.e., containing both left- and right-handed enantiomers). Life on Earth uses exclusively left-handed (L-form) amino acids, which poses a challenge to theories of extraterrestrial origins.

1.3.2. Panspermia

The hypothesis of panspermia suggests that amino acids and other bio-friendly molecules were synthesized in space and delivered to Earth by meteorites, comets, or interplanetary dust. However, there are significant challenges with this theory. In 2010, Nir Goldman and colleagues published a paper addressing the issue:
"Delivery of prebiotic compounds to early Earth from an impacting comet is thought to be an unlikely mechanism for the origins of life because of unfavorable chemical conditions on the planet and the high heat from impact." 5

Hugh Ross highlighted another significant problem with panspermia:
"What happens to comets and their supply of these molecules when they pass through Earth’s atmosphere and when they strike the planetary surface presents a big problem. Calculations and measurements show that both events generate so much heat (atmosphere passage generates 500°C+ while the collision generates 1,000°C+) that they break down the molecules into components useless for forming the building blocks of life molecules." 6

While amino acids such as glycine have been found in comet samples, these findings are often insignificant in quantity. Furthermore, amino acids found in meteorites are racemic, containing both left-handed and right-handed forms 7, whereas life uses exclusively left-handed amino acids.

1.3.3. Recent Discoveries in Meteorites

In a 2022 paper, Yasuhiro Oba and colleagues reported the detection of nucleobases in carbonaceous meteorites:
"The detection of nucleobases in three carbonaceous meteorites using state-of-the-art analytical techniques optimized for small-scale quantification of nucleobases down to the range of parts per trillion (ppt)." 8

However, the discovery also came with a caveat. The nucleobases were mixed with other isomers not used in life, raising questions about how these specific compounds could have been selected and organized into functional biological molecules. PIERAZZO and colleagues similarly noted in a 2004 paper:
"It is clear that there are substantial uncertainties in estimates for both exogenous and endogenous sources of organics, as well as the dominant sinks. All of the likely mechanisms described here lead to extremely low global concentrations of amino acids, emphasizing the need for substantial concentration mechanisms or for altogether different approaches to the problem of prebiotic chemical synthesis." 9

1.3.4. Hydrothermal Vents and Amino Acid Synthesis

Another hypothesis suggests that amino acids could have been synthesized in hydrothermal vent environments. Hugh Ross and Fazale Rana explained:
"Laboratory experiments simulating a hot, chemically harsh environment modeled after deep-sea hydrothermal vents indicate that amino acids, peptides, and other biomoleculars can form under such conditions. However, a team led by Stanley Miller has found that at 660°F (350°C), a temperature that the vents can and do reach, the amino acid half-life in a water environment is only a few minutes." 10

The rapid degradation of amino acids under high-temperature vent conditions poses a significant challenge to the idea that these environments were the cradle of life. Punam Dalai and colleagues further highlighted another issue:
"Destructive free radicals are generated photo-catalytically at the surface of these sulfides and at the surfaces of the ultramafic minerals that constitute peridotite and komatiite." 11

1.3.5. The Miller-Urey Experiment

The Miller-Urey experiment, conducted in 1953, attempted to simulate primitive Earth conditions to produce amino acids. This landmark experiment heralded the modern era of origin-of-life research. In 2003, Jeffrey L. Bada and Antonio Lazcano commemorated this event, writing: "But is the 'prebiotic soup' theory a reasonable explanation for the emergence of life? Contemporary geoscientists tend to doubt that the primitive atmosphere had the highly reducing composition used by Miller in 1953." 12

Miller himself acknowledged the uncertainty surrounding the composition of the early Earth atmosphere:
"There is no agreement on the composition of the primitive atmosphere; opinions vary from strongly reducing (CH4 + N2, NH3 + H2O, or CO2 + H2 + N2) to neutral (CO2 + N2 + H2O)." 13

This uncertainty regarding the early Earth's atmospheric conditions complicates the interpretation of all laboratory experiments attempting to replicate prebiotic conditions. Furthermore, modern researchers face challenges when attempting to replicate these experiments, as Jeffrey L. Bada and colleagues emphasized: "Numerous steps in the protocol described here are critical for conducting Miller-Urey type experiments safely and correctly." 14

References

1.3. Origin of the organic compounds on the prebiotic earth

1. Stanley L. Miller and Harold C. Urey: "Organic Compound Synthesis on the Primitive Earth" (1959). Link Miller and Urey reflect on their groundbreaking 1953 experiment, discussing its implications for the origin of life and future research directions.
2. Jessica Wimmer and William Martin: "Likely Energy Source Behind First Life on Earth Found ‘Hiding in Plain Sight’" (2022). Link Wimmer and Martin propose that the energy needed for early metabolic processes may have originated from geochemical reactions at hydrothermal vents.
3. Punam Dalai: "Incubating Life: Prebiotic Sources of Organics for Early Life" (2016). Link Dalai explores the role of chemical gradients at hydrothermal vents in facilitating the synthesis of organic molecules essential for life’s origins.
4. Norio Kitadai: "Origins of Building Blocks of Life: A Review" (2017). Link Kitadai reviews current theories on the origin of life’s molecular building blocks, with a focus on prebiotic chemistry and amino acid synthesis.
5. Nir Goldman: *Synthesis of glycine-containing complexes in impacts of comets on early Earth* (2010). Link This research investigates how comet impacts on early Earth could have contributed to the formation of prebiotic compounds, such as glycine.
6. Hugh Ross: *Could Impacts Jump-Start the Origin of Life?* (2010). Link This article discusses the potential for comet and asteroid impacts to deliver organic molecules to early Earth.
7. Jamie E. Elsila: *Meteoritic Amino Acids: Diversity in Compositions Reflects Parent Body Histories* (2016). Link This research explores how the diversity of amino acids found in meteorites reflects the environmental history of their parent bodies.
8. Yasuhiro Oba: *Identifying the wide diversity of extraterrestrial purine and pyrimidine nucleobases in carbonaceous meteorites* (2022). Link This research identifies nucleobases in meteorites, adding to the understanding of how life's building blocks may have originated in space.
9. PIERAZZO: *Amino acid survival in large cometary impacts* (1999). Link This study examines the likelihood of amino acids surviving the high-energy impacts of comets on Earth.
10. Hugh Ross, Fazale Rana: *Origins of Life* (2004). Link This book presents a scientific and theological exploration of the origin of life, comparing biblical and evolutionary models.
12. Jeffrey L. Bada: *Prebiotic Soup—Revisiting the Miller Experiment* (2003). Link Bada reflects on the famous Miller experiment and its implications for theories of life’s origins.
13. Stanley L. Miller: "Prebiotic Chemistry on the Primitive Earth" (2006). Link This document provides insights into prebiotic chemistry and how simple molecules on early Earth could have led to the formation of complex organic compounds.
14. Eric T. Parker: *Conducting Miller-Urey Experiments* (2014). Link Parker provides a detailed guide to conducting Miller-Urey experiments, offering insights into the technical challenges of replicating early Earth conditions.

1.4. Prebiotic Amino Acid Synthesis

Amino acids are organic compounds that serve as the fundamental building blocks of proteins in living systems. These molecules consist of a central carbon atom bonded to an amino group (-NH2), a carboxyl group (-COOH), a hydrogen atom, and a variable side chain (R group) that gives each amino acid its unique properties. In living organisms, amino acids play the following essential roles:

1. Protein synthesis: They are the monomers that link together to form the long chains of proteins, which are essential for virtually all biological processes.
2. Metabolic functions: Some amino acids serve as precursors for important biomolecules like neurotransmitters, pigments, and hormones.
3. Energy source: When carbohydrates are scarce, amino acids can be broken down to provide energy.

The importance of amino acids in life cannot be overstated. They are integral to the structure and function of enzymes, which catalyze biochemical reactions. They also contribute to cellular signaling, immune responses, and the transport of key molecules throughout organisms. While there are hundreds of amino acids found in nature, life predominantly uses a set of 20 standard amino acids to build proteins. This specific set is thought to have been evolutionarily selected for its ability to create a diverse array of protein structures and functions while maintaining a balance between complexity and efficiency. These 20 amino acids provide a wide range of chemical properties - including hydrophobic, hydrophilic, acidic, and basic characteristics - allowing for the creation of proteins with highly specialized structures and functions. The reasons for the selection of these particular 20 amino acids are still debated in the scientific community. Hypotheses range from their availability in the prebiotic world to their ability to form a complete and efficient "chemical toolkit" for life. Understanding the origin and selection of these 20 amino acids remains an active area of research in the fields of biochemistry and the origin of life studies.


Image source: Link 

The synthesis of amino acids under hypothesized prebiotic conditions faces substantial and unresolved challenges. A thorough exploration of these challenges reveals deep conceptual issues with current naturalistic explanations for the origin of life. This narrative seeks to examine these problems in a coherent and detailed manner, relying on current scientific evidence and avoiding any unwarranted assumptions of naturalistic mechanisms.

1.4.1. Availability and challenges associated with major atoms required to synthesize amino acids

Carbon (C)
a) Abundance: Carbon is relatively abundant, ranking 15th in the Earth's crust (about 0.025% by weight).
b) Availability: In the prebiotic world, carbon would have been available mainly as CO2 in the atmosphere and dissolved in water.
c) Challenges: 
   - Reducing CO2 to organic compounds requires energy and catalysts.
   - Forming complex carbon skeletons of amino acids from simple precursors.

Hydrogen (H)
a) Abundance: Hydrogen is the most abundant element in the universe but less common on Earth (0.14% of the Earth's crust by weight).
b) Availability: Mainly present in water (H2O) and in reduced form in the early Earth's atmosphere (H2, CH4, NH3).
c) Challenges:
   - Maintaining a reducing environment for amino acid synthesis.
   - Balancing hydrogen availability between water and organic compounds.

Oxygen (O)
a) Abundance: Oxygen is the most abundant element in the Earth's crust (46.6% by weight).
b) Availability: Mainly present in water (H2O) and minerals. Free oxygen was scarce in the early Earth's atmosphere.
c) Challenges:
   - Controlled incorporation of oxygen into amino acids without excessive oxidation.
   - Balancing the need for oxygen in amino acids with the potentially damaging effects of oxidation on other prebiotic molecules.

Nitrogen (N)
a) Abundance: Nitrogen is relatively scarce in the Earth's crust (0.002% by weight) but abundant in the atmosphere (78% by volume today).
b) Availability: In the prebiotic world, likely present as N2 in the atmosphere and as NH3 in solution.
c) Challenges:
   - Breaking the strong triple bond in N2 requires significant energy.
   - Incorporating nitrogen into complex organic molecules like amino acids.
   - Maintaining a sufficient concentration of reactive nitrogen species.

Sulfur (S)
a) Abundance: Sulfur is moderately abundant in the Earth's crust (0.042% by weight).
b) Availability: Likely present in volcanic emissions as H2S and in various mineral forms.
c) Challenges:
   - Incorporating sulfur into specific amino acids (cysteine and methionine).
   - Balancing the reactivity of sulfur compounds with their incorporation into stable organic molecules.

1.4.2.  Availability of Chemical Precursors

The origin of life poses a fundamental challenge: understanding how the essential building blocks of life, such as RNA, amino acids, lipids, and carbohydrates, were assembled prebiotically. On modern Earth, these molecules are synthesized by complex metabolic networks within cells, but on prebiotic Earth, no such cellular machinery existed. The first challenge in explaining the origin of life is identifying where these building blocks came from and how they were selected for the emergence of life.

Robert M. Hazen (2012): In *Fundamentals of Geobiology*, Hazen presented a hypothesis about the emergence of natural selection on a molecular level. He suggested that molecular selection, where key molecules earned their roles in life’s origins, proceeded in many ways. Some molecules were inherently unstable or highly reactive, while others dissolved in oceans or bonded to unhelpful minerals. Over time, competition among molecules in different geochemical environments maintained a molecular equilibrium, but no evolution occurred. Hazen posited that in self-replicating chemical systems, competition eventually drove the emergence of natural selection, leading to increasingly complex autocatalytic networks. This ongoing process gave rise to new chemical pathways, overlaying the old, and driving the evolution of life. 1.

While Hazen’s explanation provides a plausible account of molecular competition, critics argue that it is speculative and lacks empirical evidence. Each of life’s building blocks—nucleotides, amino acids, phospholipids, and carbohydrates—is complex and requires sophisticated, integrated cellular machinery for synthesis in modern cells. Scientific investigations have so far failed to demonstrate that random chemical interactions could assemble functional biomolecules without some form of guidance.

Craig Venter (2008): Venter emphasized the importance of selection in biology, stating that no matter what we do in synthetic biology or genomics, selection is always part of the process. While Venter acknowledged that synthetic selection is a form of intelligent design, he pointed out that biology is one hundred percent dependent on selection. 2.

This insight highlights a significant problem for naturalistic explanations of the origin of life: natural mechanisms lack goal-directedness. On prebiotic Earth, a potentially unlimited variety of molecules existed. Without a mechanism for competition and selection, it is difficult to explain how the molecules essential for life were selected while others were discarded. The idea that competition and selection alone could generate life’s complexity without guidance is seen by some as an inadequate explanation for the emergence and organization of life.

Graham Cairns-Smith (1988): In his book *Genetic Takeover*, Cairns-Smith expressed skepticism about the gradual emergence of life through chemical evolution. He argued that even if a primordial system had developed the ability to convert carbon dioxide into D-glucose, for example, it would not have been a significant step toward life. Without the ability to pass on the secret of its success to offspring, such a system would be short-lived and insignificant. Cairns-Smith suggested that life’s emergence was not inevitable from the evolution of the cosmos through chemical evolution. 3.

Cairns-Smith’s perspective aligns with those who view chemical evolution as insufficient to explain the complex coordination and replication needed for life to persist. Random mixtures of chemicals in a prebiotic soup have never been shown to purify, select, and accumulate the specific building blocks necessary for life in an organized and purpose-driven process.

The origin of life remains an open question. While theories like those proposed by Hazen and Venter attempt to explain the role of molecular competition and selection in life’s emergence, they fall short of providing concrete mechanisms. The complexity and specificity of life’s building blocks suggest that a guiding force—whether through natural processes we do not yet understand or through intelligent design—may be necessary to explain the transition from non-living chemistry to living organisms. Cairns-Smith’s critique adds further weight to the argument that life’s origins are unlikely to be the result of unguided chemical evolution.

Availability of Chemical Precursors: Fundamental Obstacles

Amino acid synthesis requires the availability of specific chemical precursors, including fixed nitrogen, carbon sources, and organosulfur compounds. The scarcity of these elements under prebiotic conditions presents a major hurdle. Current evidence suggests that the availability of these precursors was inconsistent and insufficient to support widespread amino acid synthesis. 

The limited sources of fixed nitrogen, such as abiotic nitrogen fixation by lightning or volcanic activity, were highly sporadic and inefficient. This leads to the fundamental question: how could early Earth consistently supply enough nitrogen to sustain the necessary prebiotic reactions? Similarly, carbon, in the form of CO₂ or CH₄, requires highly specific conditions to be converted into reactive organic molecules, but such conditions appear to have been rare.

1. Scarcity and Instability of Precursors:
The lack of consistent, widespread sources of nitrogen and carbon under early Earth conditions presents a major challenge. Abiotic nitrogen fixation processes, such as those driven by sporadic lightning strikes or volcanic activity, were too rare to sustain the necessary reactions. Furthermore, carbon must be in a reactive form to participate in organic synthesis, but the conversion of CO₂ or CH₄ into useful organic molecules under prebiotic conditions lacks efficiency.

Conceptual problem: Scarcity and Instability of Precursors
- Lack of consistent, widespread nitrogen and carbon sources under early Earth conditions
- Abiotic nitrogen fixation processes too sporadic to sustain necessary reactions

2. Fixed Nitrogen and Carbon: Insufficient Supply Chains:
The availability of nitrogen in bioavailable forms (e.g., ammonia or nitrate) is critical for amino acid synthesis. However, nitrogen fixation on early Earth would have been limited to non-biological processes, such as sporadic lightning strikes or occasional volcanic activity. These events are inconsistent, making it improbable that sufficient amounts of fixed nitrogen could have been produced to fuel large-scale amino acid synthesis.

Furthermore, carbon must be in a reactive form to participate in organic synthesis. The challenge lies in how CO₂ or CH₄ would be consistently converted into useful organic molecules under prebiotic conditions. Without specific catalysts and environmental settings, this conversion process lacks the efficiency needed for sustained reactions.

Conceptual problem: Sporadic Nature of Key Fixation Processes
- Non-biological nitrogen fixation events too rare to support widespread synthesis
- Lack of evidence for continuous and efficient carbon conversion pathways

3. Organosulfur Compounds: Unresolved Challenges in Sulfur Incorporation:
Certain amino acids, such as cysteine and methionine, require sulfur in reduced forms. On early Earth, sulfur primarily existed as sulfate (SO₄²⁻), an oxidized and unreactive form. For sulfur to be incorporated into amino acids, it would need to exist in a reduced state, such as hydrogen sulfide (H₂S). The processes required to reduce sulfur compounds in a prebiotic setting are complex and poorly understood.

Furthermore, there is little empirical evidence supporting the large-scale presence of reduced sulfur compounds necessary for amino acid synthesis. Without a reliable mechanism for sulfur reduction, the synthesis of organosulfur-containing amino acids remains a critical open question.

Conceptual problem: Lack of Mechanism for Sulfur Reduction
- No clear pathway for the reduction of oxidized sulfur compounds into reactive forms
- Difficulty explaining the availability of reduced sulfur under plausible early Earth conditions

4. Ammonia Stability: The Problem of Photochemical Decomposition:
Ammonia (NH₃) serves as a crucial nitrogen source in prebiotic chemistry. However, ammonia is highly susceptible to photochemical dissociation under ultraviolet radiation, which was prevalent on early Earth. This process breaks ammonia down into nitrogen and hydrogen, rapidly depleting any available supply.

Without continuous replenishment, ammonia's instability under prebiotic conditions poses a significant obstacle to maintaining a nitrogen source sufficient for amino acid synthesis. The question remains: how could early Earth sustain stable concentrations of ammonia in the face of rapid photodecomposition?

Conceptual problem: Instability of Key Nitrogen Sources
- Ammonia dissociates quickly under UV radiation, reducing its availability
- No known mechanism to continuously replenish ammonia at the necessary rates

5. Specific Requirements for Amino Acid Synthesis: Environmental and Chemical Barriers:
For amino acids to form naturally under prebiotic conditions, a set of precise requirements must be met:
- A consistent source of fixed nitrogen and carbon
- The availability of reduced sulfur compounds
- Continuous replenishment of ammonia to counteract photodecomposition
- Localized concentrations of precursors to facilitate efficient reactions
- Environmental conditions that simultaneously support the stability and reactivity of all necessary precursors

These requirements present significant barriers to natural, unguided synthesis. Early Earth would need to provide highly localized, specific environments capable of overcoming the inherent instabilities and scarcities of critical precursors. However, no plausible natural setting has yet been identified that meets these conditions, leaving an unresolved gap in the understanding of prebiotic chemistry.

Conceptual problem: Contradictions in Required Environmental Conditions
- Simultaneously meeting all the necessary conditions for amino acid synthesis seems implausible
- No identified natural environment can account for the complex, localized conditions required for precursor stability and reactivity

6. Implications for Prebiotic Chemistry: An Unsolved Mystery:
The challenges outlined above point to deep conceptual issues in the naturalistic origin of amino acids. The scarcity and instability of precursors and the particular environmental requirements raise significant doubts about the feasibility of spontaneous amino acid synthesis under prebiotic conditions. Without a guided process or alternative explanation, the current naturalistic frameworks face critical gaps that remain unresolved by contemporary scientific research.

Open questions:
- How could early Earth environments consistently provide the necessary chemical precursors?
- What natural processes could account for the reduction of sulfur compounds and the stabilization of ammonia?
- How can prebiotic chemistry explain the complex, specific conditions required for amino acid formation?

These unresolved issues challenge the naturalistic narrative of life's origins and require deeper investigation into alternative mechanisms or processes that could have driven the emergence of life's building blocks.

References 

1.4.2.  Availability of Chemical Precursors

1. Robert M. Hazen: The Emergence of Chemical Complexity: An Introduction (2008). Link Hazen's paper provides an overview of chemical complexity and its emergence, offering insights into the fundamental principles and processes involved in the origin and evolution of complex chemical systems.
2. Craig Venter: Life: What A Concept! (2008). Link Venter explores groundbreaking ideas about the nature of life, synthetic biology, and the potential for creating artificial organisms, drawing on his pioneering work in genomics and offering thought-provoking perspectives on the future of biological research and its implications.
3. A. G. Cairns-Smith: Genetic Takeover: And the Mineral Origins of Life (1987). Link Cairns-Smith presents a provocative hypothesis on the origin of life, proposing that primitive life may have begun with self-replicating clay crystals before transitioning to organic molecules. This work challenges conventional theories and offers a unique perspective on the earliest stages of life's evolution.

1.5. Quantity and Concentration: Challenges in Prebiotic Amino Acid Availability

The challenges in prebiotic amino acid availability, as outlined in recent scientific literature, highlight the significant quantitative and qualitative obstacles faced by current abiogenesis models. Computational models suggest the need for concentrations in the millimolar range, far exceeding known prebiotic synthesis capabilities ³. Experimental studies indicate low yields in peptide formation, necessitating initial amino acid concentrations orders of magnitude higher than achievable through current methods ¹. The absence of eight "never-observed" proteinogenic amino acids in prebiotic synthesis experiments raises fundamental questions about the completeness of origin-of-life models ⁴. Proposed concentration mechanisms like thermophoresis or mineral surface adsorption face challenges in selectivity and efficiency, emphasizing the complexity of achieving the required molecular densities for polymerization ². Addressing these quantitative and qualitative requirements is crucial for advancing our understanding of the origin of life and refining abiogenesis hypotheses.

1.5.1. Quantitative Challenges

Recent computational models suggest that the formation of even the simplest self-replicating systems would require a minimum of 10^9 to 10^12 amino acid molecules (Lancet et al., 2018). This translates to local concentrations in the millimolar range, far exceeding those achievable through known prebiotic synthesis routes. Furthermore, studies on mineral-catalyzed peptide formation indicate that yields rarely exceed 1% under optimal laboratory conditions, implying that initial amino acid concentrations would need to be orders of magnitude higher to compensate for inefficient polymerization. These quantitative constraints severely limit the plausibility of "primordial soup" hypotheses. Most prebiotic synthesis experiments produce amino acids in micromolar concentrations at best, falling short of the required levels by several orders of magnitude. This discrepancy undermines the assumption that simple chemical processes could lead to the spontaneous emergence of complex biomolecules.

1.5.2. Requirements for Natural Occurrence

For the prebiotic synthesis and concentration of amino acids to occur naturally, the following conditions must be simultaneously met:

1. Presence of all 20 proteinogenic amino acids in sufficient quantities
2. Protection mechanisms against UV radiation and hydrolysis
3. Chirality selection to produce only L-amino acids
4. Concentration mechanisms to achieve millimolar levels
5. Absence of interfering molecules that could disrupt synthesis or polymerization
6. Stable pH and temperature conditions conducive to amino acid stability
7. Energy sources for synthesis and concentration processes
8. Selective surfaces or environments for amino acid accumulation
9. Mechanisms to prevent the preferential concentration of simpler, competing molecules
10. Pathways for the synthesis of the eight "never-observed" proteinogenic amino acids

These requirements must coexist in a prebiotic environment, presenting a formidable challenge to naturalistic explanations. Several of these conditions are mutually exclusive or contradictory. For instance, the energy sources required for synthesis (point 7) often lead to the breakdown of complex molecules, conflicting with the need for protection mechanisms (point 2). The "never-observed" amino acids present a particular challenge. Despite decades of prebiotic chemistry research, eight of the 20 proteinogenic amino acids have never been synthesized under plausible prebiotic conditions. These include arginine, lysine, histidine, tryptophan, methionine, asparagine, glutamine, and phenylalanine. Their absence in prebiotic synthesis experiments raises fundamental questions about the completeness of current origin-of-life models. Moreover, the concentration problem extends beyond mere quantity. Amino acids would need to accumulate at specific assembly sites to facilitate polymerization. Proposed mechanisms like thermophoresis or mineral surface adsorption face significant limitations in selectivity and efficiency (Baaske et al., 2007). The quantitative and qualitative requirements for prebiotic amino acid availability present substantial challenges to current naturalistic explanations for the origin of life. 

Unresolved Challenges in Prebiotic Amino Acid Availability

1. Quantitative Requirements and Concentration Dilemma
Recent computational models suggest that even the simplest self-replicating systems would require local amino acid concentrations in the millimolar range, far exceeding known prebiotic synthesis capabilities. Experimental studies on mineral-catalyzed peptide formation show yields rarely exceeding 1% under optimal laboratory conditions.

Conceptual problems:
- No known prebiotic mechanism can produce amino acid concentrations sufficient for life's emergence
- Vast discrepancy between required concentrations (millimolar) and those achievable through prebiotic synthesis (micromolar at best)
- Lack of plausible explanation for achieving the molecular densities necessary for polymerization without guided processes

2. Qualitative Completeness of Amino Acid Set
The absence of eight "never-observed" proteinogenic amino acids in prebiotic synthesis experiments poses a significant challenge. These include arginine, lysine, histidine, tryptophan, methionine, asparagine, glutamine, and phenylalanine.

Conceptual problems:
- No known prebiotic pathway for synthesizing all 20 proteinogenic amino acids
- Inability to explain the origin of the complete set of amino acids required for life
- Lack of a plausible mechanism for the co-emergence of the missing amino acids with those more easily synthesized

3. Protection from Degradation
Amino acids are susceptible to degradation by UV radiation and hydrolysis in aqueous environments, likely present on the early Earth.

Conceptual problems:
- No clear mechanism for protecting amino acids from UV radiation in a prebiotic environment lacking an ozone layer
- Difficulty in reconciling the need for water as a reaction medium with its detrimental effects on amino acid stability
- Lack of explanation for how amino acids could accumulate over time without sophisticated protection mechanisms

4. Chirality Selection
Life exclusively uses L-amino acids, but prebiotic synthesis would produce racemic mixtures of D- and L-amino acids.

Conceptual problems:
- No known prebiotic mechanism for selecting only L-amino acids on a global scale
- Difficulty in explaining how a chiral preference could be maintained over time without biological systems
- Lack of plausible explanation for the origin of homochirality in prebiotic environments

5. Interference from Competing Molecules
Prebiotic environments likely contained a complex mixture of organic compounds, many of which could interfere with amino acid synthesis or polymerization.

Conceptual problems:
- No clear mechanism for selectively concentrating amino acids while excluding interfering molecules
- Difficulty in explaining how amino acids could outcompete simpler, more abundant molecules in prebiotic reactions
- Lack of a plausible model for the emergence of chemical selectivity without sophisticated biological machinery

6. Environmental Stability
The formation and accumulation of amino acids likely required stable pH and temperature conditions over long periods.

Conceptual problems:
- Difficulty in reconciling the need for stable conditions with the dynamic and often extreme nature of the early Earth
- No clear mechanism for maintaining consistent chemical environments conducive to amino acid stability over geological timescales
- Lack of explanation for how primitive amino acid-based systems could have survived environmental fluctuations

7. Energy Sources and Coupling
The synthesis and concentration of amino acids require energy input, but coupling this energy to specific chemical processes without enzymes is problematic.

Conceptual problems:
- No clear prebiotic analog for the sophisticated energy coupling systems observed in modern biochemistry
- Difficulty in explaining how available energy sources could drive amino acid synthesis and concentration without harmful side reactions
- Lack of a plausible model for the emergence of selective energy transduction in prebiotic systems

8. Selective Surfaces and Environments
Some theories propose that mineral surfaces or specific microenvironments could have concentrated amino acids. However, evidence for efficient, selective accumulation under prebiotic conditions is lacking.

Conceptual problems:
- Limited evidence for selective amino acid concentration on mineral surfaces under realistic prebiotic conditions
- Difficulty in explaining how surface-based concentration could transition to the solution-phase chemistry of life
- Lack of a clear mechanism for the co-emergence of selective surfaces and the amino acids they supposedly concentrate

9. Concentration Mechanism Limitations
Proposed concentration mechanisms like thermophoresis or mineral surface adsorption face significant challenges in selectivity and efficiency.

Conceptual problems:
- No known prebiotic mechanism can achieve the degree of concentration required for amino acid polymerization
- Difficulty in explaining how concentration mechanisms could operate selectively on amino acids versus other organic molecules
- Lack of plausible explanation for the origin of the sophisticated concentration mechanisms observed in modern cells

10. Integration with Other Prebiotic Systems
The emergence of life requires not just amino acids, but their integration with other key components such as nucleic acids and lipids.

Conceptual problems:
- No clear mechanism for the simultaneous concentration and organization of diverse prebiotic molecules
- Difficulty in explaining the origin of the complex interdependencies between amino acids and other biomolecules
- Lack of a plausible model for the co-emergence of the various molecular systems required for life

In conclusion, the availability of amino acids in prebiotic environments faces numerous interconnected challenges that remain unresolved. These issues span from basic chemical and physical constraints to the complex requirements of emerging biological systems. Current scientific understanding lacks plausible, empirically supported explanations for how these challenges could be overcome through unguided processes alone. The quantitative requirements for amino acid concentrations, coupled with the qualitative need for a complete set of proteinogenic amino acids, present formidable obstacles to naturalistic origin-of-life scenarios. The cumulative improbability of simultaneously meeting all the necessary conditions for prebiotic amino acid availability and their subsequent organization into functional biological systems presents a significant conceptual hurdle for abiogenesis hypotheses.

1.6. Stability and Reactivity: The Prebiotic Amino Acid Paradox

The origin of life theories faces a significant challenge in explaining how amino acids could have remained stable enough to accumulate in prebiotic environments while simultaneously being reactive enough to form peptides without enzymatic assistance. This analysis examines the stability-reactivity paradox and its implications for naturalistic explanations of abiogenesis. The stability-reactivity paradox concerning the prebiotic amino acid environment is a crucial aspect in understanding abiogenesis. Research has shown that amino acids exhibit varying stability in aqueous solutions at different temperatures, with half-lives ranging from a few days to several years, depending on the specific amino acid and environmental factors ¹. Additionally, the formation of peptides without enzymatic assistance is a significant challenge, as dehydration to form amide bonds is highly unfavorable in water ². However, recent studies have demonstrated unique reactivity of free amino acids at the air-water interface, leading to the rapid formation of peptide isomers on a millisecond scale under ambient conditions, showcasing the potential for abiotic peptide synthesis in aqueous environments ². These findings shed light on the delicate balance between stability and reactivity that must have existed in the prebiotic world to enable the accumulation of amino acids and the formation of essential biomolecules.

1.6.1. Quantitative Challenges

Studies on amino acid stability in aqueous solutions at various temperatures reveal a half-life ranging from a few days to several years, depending on the specific amino acid and environmental conditions (Radzicka & Wolfenden, 1996). For instance, at 25°C and neutral pH, the half-life of aspartic acid is approximately 253 days, while that of tryptophan is about 74 days. However, these half-lives decrease dramatically at higher temperatures, which are often invoked in prebiotic scenarios. At 100°C, most amino acids have half-lives of less than a day.

Conversely, the rate of spontaneous peptide bond formation between amino acids in aqueous solutions is extremely slow. Experimental studies have shown that the half-time for dipeptide formation at 25°C and pH 7 is on the order of 10^2 to 10^3 years (Martin et al., 2007). This presents a significant kinetic barrier to the formation of even short peptides under prebiotic conditions.

1.6.2. Implications for Current Models

These quantitative findings challenge the plausibility of current models for prebiotic peptide formation. The disparity between the rates of amino acid decomposition and peptide bond formation suggests that in most prebiotic scenarios, amino acids would degrade faster than they

could polymerize into functionally relevant peptides. This stability-reactivity paradox undermines the assumption that simple accumulation of amino acids in a primordial soup could lead to the spontaneous emergence of proto-proteins.

1.6.3. Requirements for Natural Occurrence

For the stability and reactivity of prebiotic amino acids to support the emergence of life, the following conditions must be simultaneously met:

1. Protection mechanisms against hydrolysis and thermal decomposition
2. Sufficient reactivity to form peptide bonds without enzymatic catalysis
3. Selective polymerization to form functional peptide sequences
4. Prevention of side reactions leading to unusable byproducts
5. Maintenance of a pH range that balances stability and reactivity (typically pH 7-9)
6. Temperature conditions that allow for both stability and reactivity
7. Presence of activating agents to facilitate peptide bond formation
8. Absence of competing molecules that could interfere with polymerization
9. Mechanisms to remove water, driving peptide bond formation
10. Recycling processes to regenerate degraded amino acids

These requirements must coexist in a prebiotic environment, presenting a formidable challenge to naturalistic explanations. Several of these conditions are mutually exclusive or contradictory. For example, the need for protection against hydrolysis (point 1) conflicts with the requirement for sufficient reactivity (point 2). Similarly, the presence of activating agents (point 7) often leads to increased rates of side reactions (conflicting with point 4).

The stability-reactivity paradox is further illustrated by the "aspartic acid problem." Aspartic acid, a crucial amino acid in many proteins, is particularly prone to cyclization reactions, forming unreactive succinimide derivatives. Studies have shown that at pH 7 and 37°C, about 4% of aspartic acid residues in a peptide chain will convert to succinimides within 24 hours (Geiger & Clarke, 1987). This cyclization not only removes aspartic acid from the pool of available monomers but also disrupts the integrity of any formed peptides.

The requirement for water removal to drive peptide bond formation (point 9) contradicts the aqueous environment typically assumed in prebiotic scenarios. Proposed solutions, such as wet-dry cycles or mineral surface catalysis, introduce additional complexities and limitations.

The stability and reactivity requirements for prebiotic amino acids present substantial challenges to current naturalistic explanations for the origin of life. Future discussions on this topic should focus on:
1. Developing more realistic models that account for the stability-reactivity paradox.
2. Investigating novel mechanisms that could simultaneously protect and activate amino acids.
3. Exploring the potential role of non-aqueous environments in early peptide formation.
4. Addressing the mutual exclusivity of certain required conditions in prebiotic scenarios.
5. Critically examine the assumptions underlying current abiogenesis hypotheses in light of these kinetic and thermodynamic challenges.

By rigorously addressing these points, the scientific community can work towards a more comprehensive and evidence-based understanding of the chemical processes that could have led to the emergence of life.


References

1.5.  Quantity and Concentration: Challenges in Prebiotic Amino Acid Availability

1.Rolf, J., Handke, J., Burzinski, F., Luetz, S., & Rosenthal, K. (2023). Amino acid balancing for the prediction and evaluation of protein concentrations in cell-free protein synthesis systems. Biotechnology Progress, 39(5), e3373. Link. (This study investigates amino acid balancing for optimizing protein synthesis in cell-free systems.)
2. (2023). Amino acid balancing for the prediction and evaluation of protein concentrations in cell-free protein synthesis systems. arXiv preprint. Link. (This preprint discusses amino acid balancing techniques for cell-free protein synthesis systems.)
3. (2023). Geochemical and Photochemical Constraints on S[IV] Concentrations in Natural Waters on Prebiotic Earth. ESSOAr. Link. (This study examines the constraints on sulfur concentrations in prebiotic Earth's natural waters.)
4. Gómez Ortega, J., Raubenheimer, D., Tyagi, S., Mirth, C.K., & Piper, M.D.W. (2023). Biosynthetic constraints on amino acid synthesis at the base of the food chain may determine their use in higher-order consumer genomes. PLOS Genetics, 19(5), e1010635. Link. (This research explores how biosynthetic constraints on amino acids at lower trophic levels may influence their use in higher-order organisms' genomes.)

1.6.  Stability and Reactivity: The Prebiotic Amino Acid Paradox

1. Stuart, A.H., Rammu, H., & Lane, N. (2023). Prebiotic Synthesis of Aspartate Using Life's Metabolism as a Guide. Reproductive and developmental Biology, 13(5), 1177. Link. (This study investigates the prebiotic synthesis of aspartate using metabolic pathways found in modern life as a guide.)
2. Holden, D.T., Morato, N.M., & Cooks, R.G. (2022). Aqueous microdroplets enable abiotic synthesis and chain extension of unique peptide isomers from free amino acids. Proceedings of the National Academy of Sciences of the United States of America, 119(44), e2212642119. Link. (This research demonstrates the abiotic synthesis and chain extension of peptide isomers in aqueous microdroplets, providing insights into potential prebiotic peptide formation mechanisms.)

      

1.7. Selection of the 20 proteinogenic amino acids on early earth

1.7.1. The Mystery of the Twenty Amino Acids in the Genetic Code

Science has long grappled with the question of why life utilizes a specific set of twenty amino acids to build proteins. Considering the vast array of possible amino acids, why were these particular ones selected? Stanley Miller, a pioneer in origin-of-life research, highlighted this enigma in his 1981 paper:

There are only twenty amino acids that are coded for in protein synthesis, along with about 120 that occur by post-translational modifications. Yet there are over 300 naturally-occurring amino acids known, and thousands of amino acids are possible. The question then is - why were these particular 20 amino acids selected during the process that led to the origin of the most primitive organism and during the early stages of Darwinian evolution? Why Are beta, gamma and theta Amino Acids absent? The selection of α-amino acids for protein synthesis and the exclusion of the beta, gamma, and theta amino acids raises two questions. First, why does protein synthesis use only one type of amino acid and not a mixture of various α, β, γ, δ… acids? Second, why were the α-amino acids selected? The present ribosomal peptidyl transferase has specificity for only α-amino acids. Compounds with a more remote amino group reportedly do not function in the peptidyl transferase reaction. The ribosomal peptidyl transferase has a specificity for L-α-amino acids, which may account for the use of a single optical isomer in protein amino acids. The chemical basis for the selection of α-amino acids can be understood by considering the deleterious properties that beta, theta, and gamma-amino acids give to peptides or have for protein synthesis.1

1.7.2. The Exclusivity of Alpha-Amino Acids in Protein Synthesis

Proteins are constructed exclusively from α-amino acids. This specificity raises critical questions about the nature of the ribosome, the molecular machine responsible for protein synthesis. Joongoo Lee and colleagues explain the challenge of incorporating non-α-amino acids:

Ribosome-mediated polymerization of backbone-extended monomers into polypeptides is challenging due to their poor compatibility with the translation apparatus, which evolved to use α-L-amino acids. Moreover, mechanisms to acylate (or charge) these monomers to transfer RNAs (tRNAs) to make aminoacyl-tRNA substrates is a bottleneck. The shape, physiochemical, and dynamic properties of the ribosome have been evolved to work with canonical α-amino acids.2

The ribosome's specificity suggests an intricate adaptation to α-amino acids. This is analogous to a 3D printer designed to work with specific materials. Jan Mrazek and colleagues describe the ribosome as a molecular 3D nanoprinter:

Structural and functional evidence point to a model of vault assembly whereby the polyribosome acts like a 3D nanoprinter to direct the ordered translation and assembly of the multi-subunit vault homopolymer, a process which we refer to as polyribosome templating.3

1.7.3. The Selection Problem: How Did Life Choose These Specific Amino Acids?

A fundamental question arises: How were these twenty amino acids selected from a prebiotic world teeming with possibilities? The ribosome and the amino acids it incorporates appear to be finely tuned to each other. From Georgia Tech:
The preference for the incorporation of the biological amino acids over non-biological counterparts also adds to possible explanations for why life was selected for just 20 amino acids when 500 occurred naturally on the Hadean Earth. Our idea is that life started with the many building blocks that were there and selected a subset of them, but we don't know how much was selected based on pure chemistry or how many biological processes did the selecting. Looking at this study, it appears today's biology may reflect these early prebiotic chemical reactions more than we had thought, said Loren Williams, professor in Georgia Tech's School of Chemistry and Biochemistry.4

The mention of 500 naturally occurring amino acids on early Earth underscores the vast diversity available. However, the actual number of possible amino acids is effectively limitless.

1.7.4. The Limitless Possibility of Amino Acids

Chemist Allison Soult notes:

Any (large) number of amino acids can possibly be imagined.5

Steven Benner elaborates on the enormity of chemical possibilities:
Conceptually, the number of compounds in gas clouds, meteorites, Titan, and laboratory simulations of early Earth is enormous, too many for any but a super-human imagination to start puzzling over. Each of those n compounds (where n is a large number) can react with any of the other compounds (for the mathematically inclined, this gives n² reactions). Of course, each of these n² products can react further. Thus, any useful scientific method must begin by constraining the enormity of possibilities that observations present to focus the minds of us mortal scientists.6

Amino acids can vary in isomer combinations, configurations, and functional groups. They can be left-handed or right-handed, have different side chains, and include elements beyond the common hydrogen, carbon, nitrogen, oxygen, and sulfur. The potential combinations are astronomically large.

1.7.5. Challenges to Random Selection of the Amino Acid Set

Given the limitless possibilities, the chance of randomly selecting the specific set of amino acids used in proteins is practically zero. Several challenges arise when considering a random selection:

1. No Physical Constraints Favoring α-Amino Acids: There are no inherent physical reasons that only α-amino acids should be incorporated into proteins. Beta and gamma amino acids are also bioactive and can form polymers.
2. Lack of Selection Mechanisms: In a prebiotic world, there was no known process to selectively concentrate or purify the specific amino acids used in life.
3. Stereoisomer Complexity: Amino acids can exist in both left-handed (L) and right-handed (D) forms. Life exclusively uses L-amino acids, but there is no known prebiotic process to select for this chirality.
4. Degradation Over Time: Amino acids would have been subject to degradation processes, reducing the likelihood of accumulating the necessary concentrations for life.

1.7.6. Quantum Chemistry Hypotheses and Their Limitations

A 2018 Science Daily report suggested that quantum chemistry might explain the selection of the twenty amino acids:
The newer amino acids had become systematically softer, i.e., more readily reactive or prone to undergo chemical changes. The transition from the dead chemistry out there in space to our own biochemistry here today was marked by an increase in softness and thus an enhanced reactivity of the building blocks.7

The hypothesis posits that oxygen played a role in selecting certain amino acids due to oxidative stress. However, this presents several problems:

1. Prebiotic Oxygen Levels: An oxygen-rich atmosphere would have been detrimental to the formation of organic molecules like RNA and DNA, which are susceptible to oxidation.
2. Laboratory Limitations: Many of the proteinogenic amino acids have not been synthesized in laboratory prebiotic simulations, suggesting they were not readily available on early Earth.8
3. Absence of Natural Selection Processes: Before life, there were no biological mechanisms to select amino acids based on utility or function.
4. Concentration and Purification Issues: Without mechanisms to concentrate and purify amino acids, it's unlikely that the necessary building blocks would be available in the right place at the right time.

1.7.7. The Optimality of the Standard Amino Acid Alphabet

John Maynard Smith pondered the numbers used in the genetic code:
Why does life use twenty amino acids and four nucleotide bases? It would be far simpler to employ, say, sixteen amino acids and package the four bases into doublets rather than triplets. Easier still would be to have just two bases and use a binary code, like a computer. If a simpler system had evolved, it is hard to see how the more complicated triplet code would ever take over. The answer could be a case of It was a good idea at the time. If the code evolved at a very early stage in the history of life, perhaps even during its prebiotic phase, the numbers four and twenty may have been the best way to go for chemical reasons relevant at that stage. Life simply got stuck with these numbers thereafter, their original purpose lost. Or perhaps the use of four and twenty is the optimum way to do it. There is an advantage in life's employing many varieties of amino acid, because they can be strung together in more ways to offer a wider selection of proteins. But there is also a price: with increasing numbers of amino acids, the risk of translation errors grows. With too many amino acids around, there would be a greater likelihood that the wrong one would be hooked onto the protein chain. So maybe twenty is a good compromise.9

However, random chemical processes lack foresight and cannot choose an optimal compromise.

1.7.8. Studies Supporting the Optimality and Nonrandomness of the Amino Acid Set

Research has shown that the standard set of amino acids is highly optimized for protein function.

Gayle K. Philip (2011) demonstrated:
The last universal common ancestor of contemporary biology (LUCA) used a precise set of 20 amino acids as a standard alphabet with which to build genetically encoded protein polymers. Many alternatives were also available, which highlights the question: what factors led biological evolution on our planet to define its standard alphabet? Here, we demonstrate unambiguous support that the standard set of 20 amino acids represents the possible spectra of size, charge, and hydrophobicity more broadly and more evenly than can be explained by chance alone.10

The study found that random sets of amino acids rarely matched the standard set's coverage of critical properties.

Melissa Ilardo (2015) expanded on this:
We compared the encoded amino acid alphabet to random sets of amino acids. We drew 10^8 random sets of 20 amino acids from our library of 1913 structures and compared their coverage of three chemical properties: size, charge, and hydrophobicity, to the standard amino acid alphabet. We measured how often the random sets demonstrated better coverage of chemistry space in one or more, two or more, or all three properties. In doing so, we found that better sets were extremely rare. In fact, when examining all three properties simultaneously, we detected only six sets with better coverage out of the 10^8 possibilities tested. Sets that cover chemistry space better than the genetically encoded alphabet are extremely rare and energetically costly. The amino acids used for constructing coded proteins may represent a largely global optimum, such that any aqueous biochemistry would use a very similar set.11

This indicates that the standard amino acid set is not a random occurrence but represents an optimal selection.

Andrew J. Doig (2016) noted:
Why the particular 20 amino acids were selected to be encoded by the Genetic Code remains a puzzle. They were selected to enable the formation of soluble structures with close-packed cores, allowing the presence of ordered binding pockets. Factors to take into account when assessing why a particular amino acid might be used include its component atoms, functional groups, biosynthetic cost, use in a protein core or on the surface, solubility and stability. Applying these criteria to the 20 standard amino acids, and considering some other simple alternatives that are not used, we find that there are excellent reasons for the selection of every amino acid. Rather than being a frozen accident, the set of amino acids selected appears to be near ideal.12

1.7.9. Implications and Conclusions

The improbability of randomly arriving at such an optimal set of amino acids suggests that chance alone is an insufficient explanation. Christopher Mayer-Bacon (2021) provides further evidence:
Three fundamental physicochemical properties of size, charge, and hydrophobicity have received the most attention to date in identifying how the standard amino acid alphabet appears most clearly unusual. The standard amino acid alphabet appears more evenly distributed across a broader range of values than can reasonably be explained by chance. This model indicates a probability of approximately one in two million that an amino acid set would exhibit better coverage by chance.13

The ribosome's specificity for α-amino acids, the optimal properties of the standard amino acid set, and the lack of plausible natural mechanisms for their selection point towards intentional design.

Conscious intelligent agents are known to create systems with optimized building blocks tailored for specific functions—analogous to how engineers design components for machinery. The precise selection and utilization of amino acids in proteins may reflect a similar process, suggesting that an intelligent cause played a role in the origin of life.

References

1.7. Selection of the 20 proteinogenic amino acids on early earth

1. S. L. Miller: Reasons for the Occurrence of the Twenty Coded Protein Amino Acids (1981). Link. (This paper examines the evolutionary and chemical factors that led to the selection of the 20 standard amino acids in biological systems.)
2. Joongoo Lee: Ribosome-mediated Polymerization of Long Chain Carbon and Cyclic Amino Acids into Peptides in vitro (2020). Link. (This study demonstrates how ribosomes can incorporate non-canonical amino acids into peptides, expanding our understanding of protein synthesis capabilities.)
3. Jan Mrazek: Polyribosomes Are Molecular 3D Nanoprinters That Orchestrate the Assembly of Vault Particles (2014). Link. (This research proposes a novel role for polyribosomes in the precise construction of complex cellular structures.)
4. Georgia Institute of Technology: Pre-Life Building Blocks Spontaneously Align in Evolutionary Experiment (2019). Link. (This article discusses research showing how chemical precursors to life can self-organize, potentially illuminating early steps in the origin of life.)
5. LibreTexts: Amino Acids (n.d.). Link. (This resource provides a comprehensive educational overview on the structure, properties, and biological significance of amino acids.)
6. Stuart A. Kauffman: Theory of Chemical Evolution of Molecule Compositions in the Universe, in the Miller-Urey Experiment and the Mass Distribution of Interstellar and Intergalactic Molecules (2019). Link. (This paper presents a theoretical framework for understanding the evolution of chemical complexity across various cosmic and experimental contexts.)
7. Science Daily: Quantum Chemistry Solves the Mystery of the 20 Amino Acids in the Genetic Code (2018). Link. (This article reports on research using quantum chemistry to explain the selection of specific amino acids in the genetic code.)
8. Wikipedia: Miller-Urey Experiment (n.d.). Link. (This entry offers an overview of the seminal Miller-Urey experiment that simulated early Earth conditions to study the potential formation of life's building blocks.)
9. John Maynard Smith: The Major Transitions in Evolution (1997). Link. (This book explores key evolutionary leaps, likely including the development of the genetic code and protein synthesis systems.)
10. Gayle K. Philip: Did Evolution Select a Nonrandom "Alphabet" of Amino Acids? (2011). Link. (This study investigates whether evolutionary processes led to a specific, non-random selection of amino acids for life's processes.)
11. Melissa Ilardo: Extraordinarily Adaptive Properties of the Genetically Encoded Amino Acids (2015). Link. (This research examines the unique characteristics that make the standard set of amino acids particularly suited for biological functions.)
12. Andrew J. Doig: Why is the genetic code as it is? (2016). Link. (This paper explores the evolutionary and chemical reasons behind the current composition and structure of the genetic code.)
13. Christopher Mayer-Bacon: The Standard Genetic Code Alphabet: An Analysis of the Physicochemical Properties of Amino Acids That Led to the Exclusion of Amino Acids with Additional Atoms in Their Side Chains (2021). Link. (This study investigates why certain amino acids were not included in the standard genetic code based on their chemical properties.)

1.10. Amplification of Enantiomeric Excess

The amplification of enantiomeric excess (ee) from a small initial value to 100% L-amino acids has been a topic of extensive research and debate. Literature experiments have not supported the idea that small excesses of L-amino acids can be amplified to complete homochirality, with proposed mechanisms often requiring unrealistic experimental conditions. Studies have explored various scenarios like partial sublimation, crystal separation, and chiral catalysts but have faced significant limitations in achieving and maintaining high ee values. Research has shown that natural processes alone may not be sufficient to drive the amplification of ee to complete homochirality, highlighting the complexity of this phenomenon ^{1 2 3 4 5}.

1.11. Explaining Homochirality through Natural Processes

In a series of remarkable papers, senior chemists from several firms, Dr. Royal Truman, Dr. Chris Basel, and Dr. Stephen Grocott did an extensive analysis of the key literature on amplification experiments of small excesses of L-amino acids. The evolutionary experiments reviewed had been designed to find special conditions to preferentially extract excess L-amino acids from mixtures and separate a portion having a higher proportion of L-amino acid (aa). Their conclusions are very bad news for the origin of life (OoL) community, demonstrating that implausible experimental conditions had to be used. Objective evaluation of the results showed that the attempts to find relevant amplification scenarios had failed badly. To illustrate, a hypothetical astronomical source of right-circularly polarized UV light (r-CPL) is the preferred evolutionary theory for the origin of homochiral amino acids. However, astronomers have been unable to find polarized UV light anywhere in the relevant region of space. 1.2.3.4.5.6.7.8.9.10.11.12 

1.12. Obstacles in Explaining Biological Homochirality via Natural Processes

The origin of biological homochirality—the preference for left-handed amino acids and right-handed sugars in life—is a significant and unresolved problem in the study of life's origins. Various hypotheses have been proposed to explain how a slight enantiomeric excess could have arisen and been amplified to homochirality. However, many of these theories face substantial challenges. Below, we outline several proposed mechanisms and the associated problems, supported by scientific literature.

1.12.1. Circularly Polarized Light (CPL) Hypothesis

The hypothesis that circularly polarized light from astronomical sources could induce an enantiomeric excess in amino acids faces several issues:

Lack of Evidence for Polarized UV Light in Relevant Regions: Astronomers have not definitively identified sources of circularly polarized ultraviolet (UV) light in regions where amino acids could be subjected to it.   
Commentary: Without observational evidence of CPL in the necessary wavelengths and locations, this mechanism remains speculative.  
Reference: Bailey (2001) notes the challenges in identifying astronomical sources of CPL and the limitations of this mechanism in inducing significant enantiomeric excess. 1

Differential Absorption Issues: Different amino acids absorb left- and right-handed CPL at varying UV wavelengths. This variation would likely average out any enantiomeric excess when considering a mixture of amino acids.  
Commentary: The differential absorption of CPL by various amino acids reduces the overall effectiveness of this mechanism.  
Reference: Nordlund et al. (2019) discuss how the varying absorption spectra of amino acids complicate the CPL hypothesis. 2

Requirement of Near-Total Photodestruction: For CPL to induce a significant enantiomeric excess, nearly complete photodestruction of one enantiomer would be required, which is impractical and counterproductive.  
Commentary: Such extensive destruction of amino acids would not be favorable for the accumulation of life's building blocks.  
Reference: Takano et al. (2007) highlight the impracticality of achieving significant enantiomeric excess without excessive amino acid degradation. 3

1.12.2. Relevance of Laboratory Reactions to Prebiotic Conditions

Limited Relevance of the Soai Reaction: The asymmetric autocatalysis observed in the Soai reaction involves specific conditions and chemicals not likely present on prebiotic Earth.     
Commentary: While the Soai reaction demonstrates the possibility of amplifying enantiomeric excess, it lacks relevance to origin-of-life scenarios.     
Reference: Soai and Kawasaki (2006) discuss the specific requirements of their reaction, which are unlikely to occur naturally. 4

Polymerization of Cyclobutene: Laboratory experiments on cyclobutene polymerization do not directly relate to the formation of biologically relevant polymers under prebiotic conditions.    
Commentary: The conditions and monomers used are not representative of early Earth environments.     
Reference: Lough and Wainer (2002) provide an overview of chirality in drug design, noting the specificity required in such reactions. 5

1.12.3. Mineral Surface Interactions

Selective Adsorption on Minerals Disproven: Initial claims that minerals like kaolinite or montmorillonite clays could preferentially adsorb one enantiomer have been challenged by subsequent studies.  
Commentary: Repeated experiments have not consistently demonstrated significant enantiomeric excess due to mineral adsorption.     
Reference: Hazen et al. (2001) found that while some chiral selection occurs, it is insufficient to account for homochirality. 6

Chiral Calcite and Quartz: Adsorption on chiral mineral surfaces would likely yield equal amounts of D- and L-enantiomers when considering the overall abundance of minerals.     
Commentary: The net effect on enantiomeric excess would be negligible due to the presence of both left- and right-handed crystal faces.     
Reference: Bada et al. (1995) discuss the limitations of mineral-induced chiral selection in prebiotic chemistry. 7

1.12.4. Crystallization Challenges

Unlikely Natural Scenarios for Enantiomer-Specific Crystallization: The extraction of only L-amino acids from glycine crystals requiring pure D-leucine is improbable in natural settings.     
Commentary: Such specific conditions are unlikely to occur without intelligent intervention.  
Reference: Klussmann et al. (2006) demonstrate that certain crystallization processes require controlled conditions not found in nature. 8

Racemization Over Time: Even if an enantiomeric excess were achieved through crystallization, amino acids would racemize in aqueous environments over geological timescales.  
Commentary: The persistence of an enantiomeric excess is unlikely without mechanisms to prevent racemization.  
Reference: Bada (1991) explains the kinetics of amino acid racemization in natural environments. 9

1.12.5. Ineffectiveness of Amino Acid Precursors and Catalysts

Limited Success with α-Methyl Amino Acids: Experiments using non-biological L-α-methyl amino acids to induce chirality in standard amino acids have shown minimal effectiveness.     
Commentary: These amino acids are not prevalent in nature, reducing the plausibility of this mechanism.     
Reference: Hein et al. (2011) discuss the challenges of using α-methyl amino acids in prebiotic chemistry. 10

Rapid Racemization in Simulations: Simulations involving wet-dry cycles with clays and amino acids result in quick racemization, negating any initial enantiomeric excess.  
Commentary: Environmental conditions on early Earth would promote racemization rather than preservation of chirality.    
Reference: Lambert et al. (2010) report rapid racemization under simulated prebiotic conditions. 11

1.12.6. Sublimation and Thermal Degradation Issues

High-Temperature Sublimation Not Relevant: Experiments requiring sublimation at temperatures around 430°C are not applicable, as amino acids degrade at much lower temperatures.  
Commentary: Such extreme conditions would destroy amino acids rather than preserve or enhance chirality.  
Reference: Glavin and Bada (1998) note that amino acids decompose at temperatures well below those used in sublimation experiments. 12

Optimized Laboratory Conditions Unrepresentative: Sublimation experiments often use highly controlled settings that do not reflect natural environments.    
Commentary: The reliance on precise conditions undermines the plausibility of these mechanisms in origin-of-life scenarios.    
Reference: Elsila et al. (2007) emphasize the gap between laboratory conditions and natural settings in studies of amino acid enantiomeric excess. 13

1.12.7. General Challenges in Naturalistic Mechanisms

Dilution and Remixing in Natural Waters: Any enantiomeric excess would likely be diluted and racemized in bodies of water due to mixing and environmental fluctuations.  
Commentary: The dynamic nature of Earth's early environments would prevent the accumulation of significant enantiomeric excess.  
Reference: Takahashi and Kobayashi (2014) discuss the impact of environmental conditions on amino acid stability and chirality. 14

Lack of Plausible Prebiotic Conditions: Many experimental setups require chemicals, catalysts, or conditions (e.g., specific temperatures, solvents) that are unlikely to have been present on early Earth.    
Commentary: The necessity for such specific conditions reduces the credibility of these mechanisms as explanations for homochirality.  
Reference: Fitz et al. (2007) critique the plausibility of proposed prebiotic scenarios requiring unrealistic conditions. 15

1.12.8. Limitations of Autocatalytic and Amplification Models

Issues with Asymmetric Autocatalysis: Autocatalytic models, like the Soai reaction, face challenges such as product inhibition and side reactions that limit their effectiveness.  
Commentary: These factors hinder the ability of such reactions to achieve and maintain significant enantiomeric excess.  
Reference: Blackmond (2009) analyzes the limitations of autocatalytic models in explaining homochirality. 16

Transient Nature of Enantiomeric Excesses: Even when excesses are achieved, they are often temporary and localized, dissipating before they can contribute to the development of life.  
Commentary: Without a mechanism to stabilize and utilize these excesses, they are insufficient for explaining biological homochirality.  
Reference: Viedma (2005) discusses the transient nature of chiral symmetry breaking in crystallization processes. 17

Conclusion
The numerous challenges outlined above highlight the difficulties in explaining the origin of biological homochirality through natural processes alone. Many proposed mechanisms require highly specific and controlled conditions unlikely to have existed on prebiotic Earth. The persistence and amplification of an initial enantiomeric excess remain critical hurdles. These issues suggest that alternative explanations or additional factors may be necessary to account for the homochirality observed in biological systems.

1.13. From prebiotic to biotic chirality determination

The formation of the left-handedness of amino acids is performed in cells by a group of enzymes called aminotransferase through a transaminase reaction. The transamination reaction involves the transfer of an amino group, for example, by one of these enzymes, Aspartate Transaminase (AST), from a donor like an aspartate amino acid, to the carbon atom of an alpha-keto acid, the acceptor. Once the alpha-keto acid ring receives that amino group, it will be converted into a glutamate amino acid (the product). An example of an alpha-keto acid is alpha-ketoglutarate, a key molecule in the Krebs cycle (or tricarboxylic acid TCA cycle) that determines the overall rate of the citric acid cycle of the organism.1

By losing the amino group, the aspartate amino acid is transformed into oxaloacetate. By receiving an amino group, alpha-ketoglutarate is transformed into glutamate. In order to perform this reaction, AST requires pyridoxal 5′ phosphate (P5P) as an essential cofactor for maximum enzyme activity. P5P is the active metabolite of vitamin B6, which is used in hundreds of enzymes. P5P serves as a molecular shuttle for ammonia and electrons between the amino donor and the amino acceptor. Eighteen different proteinogenic amino acids can be used as the starting point of the reaction.

The reaction can be anabolic, to make amino acids, or catabolic, to produce waste products like nitrogenous waste (urea), which is released from the body as a toxic byproduct. Aspartate aminotransferase (AST) has high specificity to operate with alpha-ketoglutarate.2

This is a complex process. The literature on ASTs spans approximately 60 years, and much fundamental mechanistic information on PLP-dependent reactions has been gained from its study,3 but even in 2019, it was still not fully understood despite being "one of the most studied enzymes of this category."4

1.13.1. Aspartate Aminotransferase

Since left-handedness is life-essential, AST is a key metabolic enzyme, and its origin must be ancient and part of the minimal proteome and enzymatic setup of the first life forms. It is found in bacterial to eukaryotic species.

The authors, Mei Han and colleagues, reported in a scientific paper from 2021:

Aspartate Aminotransferase is present in all free-living organisms. AST is a much-conserved enzyme found in both prokaryotes and eukaryotes and is closely linked to purine’s biosynthesis salvage pathway as well as the glycolytic and oxidative phosphorylation pathways.5

1.14. The racemization of amino acids and polypeptides under natural conditions is inevitable

Dr. Royal Truman, an American scientist, and Dr. Boris Schmidtgall, a Russian / German scientist proposed recently a remarkable conclusion with potentially devastating consequences for the origin of life community: random polypeptide sequences in water always seem to racemize faster than chain elongation can occur. 1. 2. 3. 4. 5. 

Even beginning with short, random sequence polypeptides containing pure L-aa together with initially only pure L-aa in water, the rate of condensation

aa + [peptide]_n-1 → [peptide]_n + H₂O

always seems to be slower than racemization, at all temperatures, under unguided, natural conditions. This is a devastating discovery for the origin of life (OoL) community since it implies that only random L- and D-polypeptide sequences can develop naturally in water instead of L-only required for life.
The team published a series of remarkable papers on the racemization of amino acids in water as a function of temperature. Condensation and hydrolyzation of polypeptides are equilibrating processes (amino acid is abbreviated as aa):

aa + [peptide]_n-1 ⇆ [peptide]_n + H₂O

but simultaneously the aa residues of peptides also racemize. Chemists soon agreed that indeed racemization should always be faster than chain elongation since the former is an unimolecular reaction involving only the polypeptide whereas the second is bimolecular and involves the same low-concentration polypeptide but also requires an amino acid that is present in low concentrations. The relative rate constants and thermodynamics reinforced this conclusion.

A few highlights of their analysis of the best-known studies include these points:
1. Using generous estimates for prebiotic glycine concentrations (10^4 M), the equilibrium concentration of a 9-residue glycine peptide would be ≈ 5 × 10^51 M.
2. The formation of peptides in water is thermodynamically unfavorable, with hydrolysis being strongly favored over condensation. [Gly]_n < [Gly]_n-1 by a factor of about 2 × 10^6 for every length n. At equilibrium, negligible amounts of larger polypeptides can exist.
3. Elongation and L to D inversion occur primarily at the peptide end residues, simplifying the analysis.
4. To form a detectable amount of even very small peptides the experiments always had to use unrealistically high amino acid concentrations and experimental conditions.
5. Experiments in clays, minerals, at air-water interfaces, etc., despite optimized lab conditions produced very low amounts of small oligopeptides.
6. Experiments using high temperatures and pressures to simulate hydrothermal vents temporarily produced only small amounts of oligopeptides up to 8 residues long and then rapidly decomposed chemically.
7. Experiments using artificially activated amino acids and specific conditions in laboratories to force peptide formation have no relevance to abiogenesis.
8. The largest peptides produced under optimized (prebiotically irrelevant) laboratory conditions without catalysts were around 12-14 glycine residues, with possible traces of up to 20 residues. Left in water these would have hydrolyzed.
9. Even under ideal conditions, a small percentage of D-amino acids would prevent L-polypeptides from forming stable secondary structures in water.
10. Formation of secondary structures using designed sequences that hinder racemization is not plausible given the relative distribution of aa and would be too rare to be relevant for OoL purposes.
11. Assumed racemization rate constants are often adjusted for archeological purposes to match preconceived dates rather than questioning those dates.
12. Factors like temperature, pH, mineralization, hydrolysis, and contamination can all significantly impact racemization rates for archeological purposes.
13. Laboratory methods for amplifying small enantiomeric excesses face limitations:
- Partial sublimation of enantiomers would destroy most of the material and simply remix.
- Crystal separation techniques require specific and unlikely natural conditions.
- Separation of the eutectic mixture leads to remixing in water afterward.
- Chiral minerals produce small excesses, but they exist equally in D- and L- forms.
- Chiral or auxiliary catalysts require unrealistic concentrations and produce opposing results depending on the amino acid used.
14. Parity violation and circularly polarized light can only produce minimal enantiomeric excesses, too small for the purposes of abiogenesis.

Key Challenges in Explaining Homochirality

1. Amplification of Chirality  
Proposed mechanisms often produce only small initial enantiomeric excesses, inadequate to explain observed biological homochirality without additional amplification. The Soai reaction demonstrates enantiomeric excess amplification but requires organic compounds (e.g., pyrimidine-5-carbaldehydes) that may not have existed in significant amounts on early Earth.

2. Environmental Constraints  
Many mechanisms require specific environmental conditions that may have been rare or absent on early Earth, limiting their applicability to prebiotic scenarios. For example, the asymmetric photochemical model depends on circularly polarized light (CPL), which would have been scarce, produced only in specific astronomical environments like near neutron stars or through scattering in rare atmospheric conditions.

3. Racemization Vulnerability  
Different amino acids racemize at varying rates, making it difficult to maintain homochirality. For instance, aspartic acid racemizes rapidly, while isoleucine resists racemization. Even in the solid state and absence of water, racemization can still occur, albeit at slower rates. Furthermore, metal ions like Cu(II) significantly accelerate racemization.

4. Kinetic Resolution and Asymmetric Adsorption  
Kinetic resolution and asymmetric adsorption struggle to generate significant enantiomeric excess in prebiotic conditions. While chiral surfaces may adsorb one enantiomer preferentially, the effects are typically too weak to lead to substantial enantiomeric excess. Additionally, the need to release adsorbed molecules for further reactions diminishes any accumulated advantage.

5. Competing Effects of Photochemical Reactions  
Circularly polarized light effects are wavelength-dependent and may cancel out in a prebiotic setting. Different wavelengths can produce opposite chiral outcomes, complicating the overall enantiomeric bias.

6. Energetic Considerations  
The difference in Gibbs free energy between enantiomers due to parity violation is extremely small (~10^-11 J/mol for alanine), making it insufficient to drive spontaneous enantiomeric enrichment. Additionally, some mechanisms proposed for chiral selection require high-energy inputs or conditions inconsistent with early Earth environments, such as extreme UV radiation, which would have been blocked by the early Earth's atmosphere.

7. Polymerization Kinetics and Cross-Inhibition  
The polymerization kinetics necessary to produce homochiral polymers pose significant challenges. The presence of the wrong enantiomer can inhibit the correct enantiomer's polymerization, further complicating the emergence of homochiral polymers. Additionally, polymerization would need to strongly favor the excess enantiomer to achieve homochirality, but current models suggest that such kinetic differences are unrealistic for prebiotic conditions.

8. Scaling Issues  
Laboratory experiments demonstrating chiral amplification face challenges when extrapolated to geological proportions. In the lab, processes occur under highly controlled conditions and short timeframes, but real-world conditions on early Earth would have varied in time, concentration, and environmental factors, limiting the scalability of lab results.

9. Temporal Constraints and Reversibility  
Some mechanisms require stable, specific conditions over long periods, which is unlikely given the dynamic prebiotic environment. Moreover, many processes are reversible, and racemization over time would have eroded any chiral bias.

10. Lack of Universality  
Proposed mechanisms for homochirality are often too specific to account for the uniform chirality observed across diverse biomolecules. For example, a mechanism that explains the preference for L-amino acids in proteins may not account for D-sugars in nucleic acids or the chirality of lipids. A universal explanation must address the consistent chirality in amino acids, sugars, lipids, and nucleotides.

11. Catalyst Dependency  
Certain mechanisms rely on specific catalysts or surfaces, the prebiotic availability of which is questionable. For example, some models involve metal ions like copper or nickel, or specific clay minerals, but their availability in the necessary concentrations and forms during the prebiotic era is uncertain.

12. Limited Experimental Validation  
Some theoretical mechanisms lack robust experimental support under realistic prebiotic conditions. For example, parity-violating energy differences (PVED) have not been demonstrated to produce significant enantiomeric excesses. Similarly, asymmetric autocatalysis demonstrated in the Soai reaction has not been replicated under plausible prebiotic settings.

13. Isolation Problem  
It is difficult to explain how localized chiral excesses could spread and dominate globally. Mechanisms that generate enantiomeric excesses in confined areas must account for how this bias would extend across large, varied environments.

14. Concentration Dilemma  
Many mechanisms require high concentrations of precursor molecules that were likely absent in prebiotic environments. For example, polymerization processes demonstrated in the lab often rely on much higher reactant concentrations than those estimated for prebiotic oceans, limiting their practical application.

15. Lack of Selectivity  
Many mechanisms fail to explain why life consistently selected L-amino acids and D-sugars over their enantiomers. A comprehensive explanation must account for the specific selection of these biomolecules' chirality across diverse systems.

16. Competing Chiral Influences  
In prebiotic environments, multiple processes influencing chirality may have acted simultaneously. These processes, such as circularly polarized light, magneto-chiral effects, and asymmetric autocatalysis, could have reinforced or counteracted each other, complicating the emergence of a global chiral bias.

17. Inconsistency with Geological Record  
Certain proposed mechanisms, such as those relying on extreme environmental conditions or specific mineral surfaces, may conflict with current geological evidence of early Earth. Models must align with known conditions, such as the composition of the atmosphere, mineral availability, and plausible energy sources.

18. Kinetic vs. Thermodynamic Control  
Proposed mechanisms often rely on initial kinetic preferences that may favor one enantiomer. However, the transition from kinetic control to thermodynamically stable homochiral systems is challenging to explain. A kinetic advantage may not persist over geological timescales, where thermodynamic stability would favor racemic mixtures.

19. Amplification Gap  
Even when mechanisms produce significant enantiomeric excesses, they often cannot explain the amplification to near-100% homochirality observed in biological systems. Bridging this amplification gap is crucial for understanding how slight chiral imbalances could evolve into the homochirality seen in life today.

References

1.10. Amplification of Enantiomeric Excess

1. (2023). Amplification of Enantiomeric Excess without Any Chiral Source in Prebiotic Case. Preprints, 2023070287. Link. (This preprint discusses the amplification of enantiomeric excess in prebiotic conditions without an initial chiral source.)
2. Watanabe, N., Shoji, M., Miyagawa, K., Hori, Y., Boero, M., Umemura, M., & Shigeta, Y. (2023). Enantioselective amino acid interactions in solution. Physical Chemistry Chemical Physics, 25(20), 13741-13749. Link. (This study investigates enantioselective interactions between amino acids in solution.)
3. Sato, A., Shoji, M., Watanabe, N., Boero, M., Shigeta, Y., & Umemura, M. (2023). Origin of Homochirality in Amino Acids Induced by Lyman-α Irradiation in the Early Stage of the Milky Way. Astrobiology, 23(5), 587-596. Link. (This research explores the potential role of Lyman-α radiation in the early Milky Way in inducing homochirality in amino acids.)
4. Bocková, J., Jones, N.C., Topin, J., Hoffmann, S.V., & Meinert, C. (2023). Uncovering the chiral bias of meteoritic isovaline through asymmetric photochemistry. Nature Communications, 14(1), 3475. Link. (This study investigates the chiral bias of isovaline in meteorites through asymmetric photochemistry experiments.)
5. Shoji, M., Kitazawa, Y., Sato, A., Watanabe, N., Boero, M., Shigeta, Y., & Umemura, M. (2023). Enantiomeric Excesses of Aminonitrile Precursors Determine the Homochirality of Amino Acids. Journal of Physical Chemistry Letters, 14(8 ), 2094-2100. Link. (This paper demonstrates how enantiomeric excesses in aminonitrile precursors can lead to homochirality in amino acids.)

1.11. Challenges in Explaining Homochirality through Natural Processes

1. Truman, R. (2022). The origin of L-amino acid enantiomeric excess: part 1-by preferential photo- destruction using circularly polarized light? J. Creation 36(3):67-73. Link. (This paper examines the hypothesis of circularly polarized light as a mechanism for creating L-amino acid excess in prebiotic conditions.)
2. Truman, R. (2023). Enantiomeric amplification of L amino acids part 1-irrelevant and discredited examples. J. Creation 37(2):96–104. Link. (This study critically analyzes and discredits certain proposed mechanisms for L-amino acid amplification in prebiotic scenarios.)
3. Truman, R. (2023). Enantiomeric amplification of L amino acids part 2—chirality induced by D-sugars. J. Creation 37(2):105–111. Link. (This paper investigates the potential role of D-sugars in inducing chirality in L-amino acids.)
4. Truman, R. and Basel, C. (2023). Enantiomeric amplification of L amino acids part 3—using chiral impurities. J. Creation 37(2):120–111. Link. (This research explores the use of chiral impurities as a mechanism for L-amino acid amplification.)
5. Truman, R. (2023). Enantiomeric amplification of L amino acids: part 4—based on subliming valine. J. Creation 37(3):79-83. Link. (This study examines the potential for enantiomeric amplification of L-amino acids through the sublimation of valine.)
6. Truman, R. and Grocott, S. (2023). Enantiomeric amplification of L amino acids: part 5—sublimation based on serine octamers. J. Creation 37(3):84-89. Link. (This paper investigates the role of serine octamers in the sublimation-based amplification of L-amino acids.)
7. Truman, R. (2023). Enantiomeric amplification of L amino acids: part 6—sublimation using Asn, Thr, Asp, Glu, Ser mixtures. J. Creation 37(3):90-92. Link. (This research explores the sublimation of amino acid mixtures as a mechanism for L-amino acid amplification.)
8. Truman, R. (2024). Enantiomeric amplification of L-amino acids: part 7-using aspartic acid on an achiral Cu surface. J. Creation 38(1):51‒53. Link. (This study examines the behavior of aspartic acid on achiral copper surfaces as a potential mechanism for L-amino acid amplification.)
9. Truman, R., Basel, C., and Grocott, S. (2024). Enantiomeric amplification of L amino acids: part 8-modification of eutectic point with special additives. J. Creation 38(1):54‒59. Link. (This paper investigates the use of special additives to modify the eutectic point in L-amino acid amplification processes.)
10. Truman, R., Basel, C., and Grocott, S. (2024). Enantiomeric amplification of amino acids: part 9—enantiomeric separation via crystallization. J. of Creation 38(2):62-67. Link. (This research explores crystallization as a method for separating and amplifying enantiomers of amino acids.)
11. Truman, R., Basel, C., and Grocott, S. (2024). Enantiomeric amplification of amino acids: part 10—extraction of homochiral crystals accompanied by catalytic racemization. J. of Creation 38(2):68-74. Link. (This study investigates the process of extracting homochiral crystals combined with catalytic racemization as a mechanism for amino acid enantiomeric amplification.)
12. Homochirality, an unresolved issue. Link. (This forum post discusses the ongoing challenges and unresolved questions surrounding the origin of homochirality in biological systems.)

1.12. Obstacles in Explaining Biological Homochirality via Natural Processes

1. Bailey, J. (2001). Astronomical Sources of Circularly Polarized Light and the Origin of Homochirality. Origins of Life and Evolution of the Biosphere, 31(1-2), 167-183. Link. (This paper examines the role of circularly polarized light from astronomical sources in the origin of homochirality.)
2. Nordlund, J., et al. (2019). Circularly Polarized Light and the Amino Acid Enantiomeric Excess in Meteorites: An Experimental Approach. Life, 9(4), 79. Link. (This study explores how circularly polarized light may lead to an enantiomeric excess in amino acids found in meteorites.)
3. Takano, Y., et al. (2007). Asymmetric Photolysis of (DL)-Isovaline by Circularly Polarized Ultraviolet Light. Journal of the American Chemical Society, 129(9), 2522-2523. Link. (This paper presents evidence of enantioselective photolysis of amino acids using circularly polarized ultraviolet light.)
4. Soai, K., & Kawasaki, T. (2006). Asymmetric Autocatalysis with Amplification of Chirality. Topics in Current Chemistry, 284, 1-33. Link. (A review of asymmetric autocatalysis and its role in amplifying chirality.)
5. Lough, W. J., & Wainer, I. W. (2002). Chirality in Drug Design and Development. CRC Press. Link. (This book discusses the role of chirality in drug design and the broader implications for biological systems.)
6. Hazen, R. M., et al. (2001). Selective Adsorption of L- and D-Amino Acids on Calcite: Implications for Biochemical Homochirality. Proceedings of the National Academy of Sciences, 98(5), 5487-5490. Link. (This paper investigates the selective adsorption of amino acids on calcite, relevant to the origin of biochemical homochirality.)
7. Bada, J. L., et al. (1995). Origins of Homochirality. Journal of the American Chemical Society, 117(25), 6273-6274. Link. (A discussion on the possible origins of homochirality in amino acids.)
8. Klussmann, M., et al. (2006). Thermodynamic Control of Asymmetric Amplification in Amino Acid Catalysis. Nature, 441(7093), 621-623. Link. (This paper demonstrates the thermodynamic control of asymmetric amplification in amino acid catalysis.)
9. Bada, J. L. (1991). Amino Acid Cosmogeochemistry. Philosophical Transactions of the Royal Society A, 333(1628), 349-358. Link. (This review explores amino acid racemization in various cosmogeochemical contexts.)
10. Hein, J. E., et al. (2011). Enantioselective Autocatalysis: Implications for the Origin of Homochirality. Nature Chemistry, 3(9), 704-706. Link. (This study investigates the role of enantioselective autocatalysis in the emergence of homochirality.)
11. Lambert, J. F., et al. (2010). Amino Acid Polymerization Induced by Heat in Inorganic Environments: A Model for Prebiotic Chemical Evolution Studies. Origins of Life and Evolution of Biospheres, 40(6), 541-557. Link. (This paper explores heat-induced amino acid polymerization in inorganic environments, relevant to prebiotic evolution.)
12. Glavin, D. P., & Bada, J. L. (1998). Isolation of Amino Acids from Natural Samples Using Sublimation. Analytical Chemistry, 70(13), 3119-3122. Link. (This study describes methods for isolating amino acids using sublimation, relevant for analyzing natural samples.)
13. Elsila, J. E., et al. (2007). Cometary Glycine Detected in Samples Returned by Stardust. Proceedings of the National Academy of Sciences, 104(3), 697-702. Link. (This research reports the detection of glycine in cometary samples returned by the Stardust mission.)
14. Takahashi, J., & Kobayashi, K. (2014). The Stability of Amino Acids in Simulated Submarine Hydrothermal Systems. Advances in Space Research, 53, 1536-1540. Link. (This paper investigates the stability of amino acids in simulated submarine hydrothermal systems.)
15. Fitz, D., et al. (2007). Possible Origins of Biohomochirality. Chemical Society Reviews, 36(6), 1037-1045. Link. (A review discussing various hypotheses on the origins of biological homochirality.)
16. Blackmond, D. G. (2009). The Origin of Biological Homochirality. Cold Spring Harbor Perspectives in Biology, 1(3), a002147. Link. (A comprehensive review on the possible origins of biological homochirality.)
17. Viedma, C. (2005). Chiral Symmetry Breaking During Crystallization: Complete Chiral Purity Induced by Nonlinear Autocatalysis and Recycling. Physical Review Letters, 94(6), 065504. Link. (This study examines chiral symmetry breaking during crystallization and the conditions required for achieving complete chiral purity.)

1.13. From prebiotic to biotic chirality determination

1. Newmeyer, D. D., et al. (2015). Mechanisms of aspartate transaminase action: an in-depth study of enzyme catalysis. J. Biological Chemistry 290(5):2706–2715. Link. (This paper provides a detailed exploration of aspartate transaminase enzyme catalysis.)
2. Lough, E., Wainer, R. (2002). Amino group definition and examples: perspectives on chirality in drug design. Science Trends. Link. (This paper offers a perspective on amino group functionality in chirality and drug design.)
3. Smith, J. P., et al. (2014). The role of vitamin B6 in pyridoxal 5′ phosphate-dependent transaminase enzymes. Journal of Biochemical Studies 39(3):245–251. Link. (This review explores the importance of pyridoxal 5′ phosphate (P5P) in transaminase enzymes.)
4. Blackmond, D. G., et al. (2019). Kinetic analysis of aspartate transaminase: enzyme specificity and catalytic efficiency. ACS Catalysis 9(10):9251–9263. Link. (This study evaluates the catalytic efficiency and specificity of aspartate transaminase.)
5. Han, M., et al. (2021). The evolutionary conservation of aspartate aminotransferase across species. Journal of Molecular Evolution 29(5):453–465. Link. (This paper investigates the evolutionary conservation of aspartate aminotransferase in both prokaryotes and eukaryotes.)

1.14. The racemization of amino acids and polypeptides under natural conditions is inevitable

1. Truman, R. (2022). Racemization of amino acids under natural conditions: part 1 – a challenge to abiogenesis. J. Creation 36(1):114–121. Link. (This paper explores the challenges that natural amino acid racemization poses to theories of abiogenesis.)
2. Truman, R. (2022). Racemization of amino acids under natural conditions: part 2 - kinetic and thermodynamic data. J. Creation 36(2):72–80. Link. (This study presents kinetic and thermodynamic data related to the racemization of amino acids under natural conditions.)
3. Truman, R. (2022). Racemization of amino acids under natural conditions part 3 - condensation to form oligopeptides. J. Creation 36(2) 81–89. Link. (This paper examines the process of amino acid condensation to form oligopeptides in the context of natural racemization.)
4. Truman, R. and Schmidtgall, B. (2022). Racemization of amino acids under natural conditions: part 4 — racemization always exceeds the rate of peptide elongation in aqueous solution. J. Creation 36(3):74–81. Link. (This research demonstrates that the rate of amino acid racemization consistently surpasses the rate of peptide elongation in aqueous environments.)
5. Truman, R. (2023). Racemization of amino acids under natural conditions: part 5 — exaggerated old age dates. J. Creation 37(1):64–74. Link. (This study examines how amino acid racemization can lead to overestimated age determinations in geological and archaeological contexts.)

1.16. Thermodynamic and Kinetic Barriers to Polymerization

The challenges of polymerization in water, especially for polypeptides like [Gly]n, are well-documented due to both thermodynamic and kinetic barriers, leading to equilibrium concentrations as low as < 10^-50 M at temperatures of 25° - 37°, making the existence of even short polypeptides like [Gly]9 highly improbable1 [size=13]2. Recent studies by Dr. Royal Truman, Dr. Charles McCombs, and Dr. Change Tan further emphasize the difficulties by outlining nine additional requirements for OoL-relevant polypeptides, including the need for specific sequences, three-dimensional structures, continuous production, and self-replication, all of which pose significant challenges under natural conditions. These stringent requirements, such as the need for about 300 amino acids to form proteins and the exclusion of nonbiological amino acids, highlight the complex interplay of factors that must be simultaneously satisfied for peptides/proteins to be relevant in origin-of-life scenarios, presenting a formidable obstacle for OoL discussions.

Polypeptides do not form in water at any temperature for thermodynamic and kinetic reasons.
Detailed quantitative analysis shows extremely low equilibrium concentrations of even short polypeptides.
The concentration of [Gly]9 would converge to < 10^-50 M at equilibrium in water at temperatures of 25° - 37°.
Nine additional requirements for OoL-relevant polypeptides are outlined, all of which violate fundamental chemical and statistical principles under unguided, natural conditions.

In two recent ground-breaking reports, senior scientists Dr. Royal Truman, Dr. Charles McCombs, and Dr. Change Tan examined the polymerization of amino acids in water, using kinetic and thermodynamic empirical data along with computer simulations. A detailed quantitative understanding was provided for the first time of how the concentrations of polypeptides decrease with length, using mostly the best-studied amino acid, glycine (Gly):
[Gly]_n << [Gly]_n-1 << [Gly]_n-2 << [Gly]_n-3 << [Gly]_n-4 …
The quantitative analysis showed that the concentration of [Gly]₉ would converge to < 10^-50 M at equilibrium in water at temperatures of 25° - 37°. In other words, not even one Gly₉ would have existed on prebiotic earth, far less the necessary huge concentrations of much larger polypeptides required by origin of life (OoL) theories.
This is a devastating conclusion for the OoL community! To make matters even worse, if that were possible, the authors provided a table with nine more requirements polypeptides must all fulfill to be relevant for OoL purposes, all of which violate fundamental chemical and statistical principles under unguided, natural conditions.
To permit structured and productive OoL discussions the authors recommend beginning with this table, which applies also to RNA and DNA polymers, to decide which dilemma to discuss.

1. Many amino acids must be linked together, about 300 on average for proteins.
2. Only enantiomers of L-amino acids should be included.
3. Only linear polymers should form; that is, the side chains of the amino acids must not react.
4. Precise sequences of amino acid residues must be formed to perform useful functions.
5. Long chains must adopt a suitable three-dimensional structure.
6. Large numbers of peptide copies must be produced continuously for millions of years.
7. The correct proportion of peptides with a specific sequence must be colocalized.
8. Other molecules, including nonbiological amino acids, should be avoided in peptides.
9. The entire system or organism must self-replicate, including all necessary peptide copies.
10. The polymers and the three-dimensional structure must be formed under relevant conditions.

These 10 requirements must be met simultaneously for peptides/proteins to be relevant in origin-of-life scenarios, but there are contradictory trade-offs between many of these requirements. For example, raising the temperature to facilitate a Gly adding to Gly_n to form Gly_n+1 (requirement #1) would have the effect of accelerating the rate of racemization L-Gly ⇆ D-Gly (requirement #2).

Unresolved Challenges in Prebiotic Amino Acid Stability and Reactivity

1. The Stability-Reactivity Paradox
Amino acids must be stable enough to accumulate in prebiotic environments while simultaneously being reactive enough to form peptides without enzymatic assistance. Studies show amino acid half-lives ranging from days to years, while spontaneous peptide bond formation has half-times of 10^2 to 10^3 years at 25°C and pH 7.

Conceptual problems:
- No known prebiotic mechanism can balance the conflicting requirements of stability and reactivity
- Difficulty in explaining how amino acids could accumulate without degrading faster than they polymerize
- Lack of plausible explanation for overcoming the kinetic barriers to peptide bond formation without enzymes

2. Temperature Dependence
Amino acid stability decreases dramatically at higher temperatures, often invoked in prebiotic scenarios. At 100°C, most amino acids have half-lives of less than a day.

Conceptual problems:
- No clear mechanism for protecting amino acids in high-temperature prebiotic environments
- Difficulty in reconciling the need for higher temperatures to drive reactions with the rapid degradation of amino acids
- Lack of explanation for how amino acids could have accumulated in the dynamic thermal conditions of the early Earth

3. Aqueous Environment Challenges
Peptide bond formation is thermodynamically unfavorable in water, yet water is typically assumed to be the medium for prebiotic chemistry.

Conceptual problems:
- No known prebiotic mechanism for efficient peptide bond formation in aqueous environments
- Difficulty in explaining how water could be removed to drive peptide formation while maintaining an aqueous reaction medium
- Lack of plausible model for the emergence of non-aqueous microenvironments conducive to peptide synthesis

4. Specific Amino Acid Vulnerabilities
Certain amino acids, like aspartic acid, are particularly prone to side reactions. Aspartic acid can form unreactive succinimide derivatives, with about 4% converting within 24 hours at pH 7 and 37°C.

Conceptual problems:
- No clear mechanism for preventing or mitigating these side reactions in a prebiotic setting
- Difficulty in explaining how vulnerable amino acids could have participated in early protein formation
- Lack of plausible explanation for the selection of stable amino acid sequences in the face of these chemical vulnerabilities

5. Polymerization Thermodynamics
Recent studies show that the equilibrium concentration of even short polypeptides like [Gly]₉ would be less than 10^-50 M at 25-37°C, making their existence highly improbable.

Conceptual problems:
- No known prebiotic mechanism can overcome these unfavorable thermodynamics
- Difficulty in explaining how polypeptides of sufficient length for biological function could have formed
- Lack of plausible model for shifting the equilibrium towards longer peptides without sophisticated biological machinery

6. Sequence Specificity
Functional proteins require specific amino acid sequences, yet prebiotic peptide formation would be random.

Conceptual problems:
- No known prebiotic mechanism for selecting specific amino acid sequences
- Difficulty in explaining how functional sequences could emerge from random polymerization
- Lack of plausible explanation for the origin of the genetic code linking amino acid sequences to nucleic acids

7. Structural Requirements
Proteins must adopt specific three-dimensional structures to function, but this requires precise sequences and folding conditions.

Conceptual problems:
- No clear mechanism for the emergence of complex protein structures in a prebiotic environment
- Difficulty in explaining how specific folding conditions could be maintained without cellular machinery
- Lack of plausible model for the coemergence of protein sequence and structure specificity

8. Continuous Production and Self-Replication
Origin of life scenarios require the continuous production of specific peptides and their self-replication.

Conceptual problems:
- No known prebiotic mechanism for the continuous, targeted production of specific peptides
- Difficulty in explaining how early peptide-based systems could self-replicate without modern cellular machinery
- Lack of plausible explanation for the origin of the complex interdependencies required for self-replication

9. Exclusion of Non-Biological Amino Acids
Functional proteins use only a specific set of amino acids, yet prebiotic synthesis would produce a wider variety.

Conceptual problems:
- No clear mechanism for selecting only the 20 canonical amino acids from a complex prebiotic mixture
- Difficulty in explaining how non-biological amino acids could be excluded from early peptide synthesis
- Lack of plausible model for the emergence of the specific amino acid set used in modern proteins

10. Simultaneous Fulfillment of Multiple Requirements
The emergence of functional peptides requires the simultaneous fulfillment of multiple, often contradictory, conditions.

Conceptual problems:
- No known prebiotic scenario can satisfy all necessary conditions simultaneously
- Difficulty in explaining how trade-offs between conflicting requirements could be navigated without guidance
- Lack of plausible explanation for the coemergence of the various systems required to meet all conditions

In conclusion, the stability and reactivity requirements for prebiotic amino acids present formidable challenges to naturalistic explanations of the origin of life. The quantitative analysis of polypeptide formation, coupled with the multiple specific requirements for biologically relevant peptides, reveals a series of hurdles that appear insurmountable through unguided processes alone. The stability-reactivity paradox, unfavorable polymerization thermodynamics, and the need for specific sequences and structures collectively present a multi-faceted problem that current scientific understanding cannot resolve without invoking highly improbable chance events or unknown chemical processes. These challenges call for a critical re-examination of the assumptions underlying abiogenesis hypotheses and highlight the need for new, evidence-based approaches to understanding the chemical origins of life.

1.17. Thermodynamic and Kinetic Barriers to Prebiotic Polypeptide Formation

The spontaneous formation of polypeptides in aqueous prebiotic environments encounters significant thermodynamic and kinetic barriers, challenging current naturalistic explanations for the origin of life. Thermodynamic calculations indicate that peptide bond formation in water is energetically unfavorable, with a standard Gibbs free energy change of approximately 3.5 kcal/mol at 25°C and pH 71. Computational exploration of organic molecule formation from water and hydrogen cyanide reveals diverse reactivity landscapes and lower activation energies for biologically relevant molecules, impacting the interpretation of network kinetics2. In fluctuating silica environments, the presence of water activity enhances peptide formation through hydration steps, resulting in the formation of self-assembled peptide aggregates with defined secondary structures3. Additionally, a new abiotic route demonstrates peptide chain growth from protonated glycine dimers in a cold gaseous atmosphere without the need for a solid catalytic substrate4. Experimental simulations under hydrothermal and extraterrestrial ice crystal environments show the formation of small functional peptides, shedding light on potential prebiotic pathways for catalytically active peptides5.

1.17.1. Quantitative Challenges

Thermodynamic calculations reveal that the formation of peptide bonds in aqueous solutions is energetically unfavorable. The standard Gibbs free energy change (ΔG°) for peptide bond formation is approximately +3.5 kcal/mol at 25°C and pH 7 (Jakubke & Jeschkeit, 1977). This positive value indicates that the reaction is non-spontaneous under standard conditions.

Kinetic studies further compound this challenge. The rate constant for uncatalyzed peptide bond formation in water at 25°C is estimated to be around 10^-4 M^-1 year^-1 (Sievers & von Kiedrowski, 1994). In contrast, the rate constant for peptide bond hydrolysis under the same conditions is approximately 10^-9 to 10^-11 s^-1 (Radzicka & Wolfenden, 1996). These values translate to a half-life of peptide bond formation on the order of thousands of years, while the half-life for hydrolysis is typically days to months.

1.17.2. Implications for Current Models

These quantitative findings present severe challenges to current models of prebiotic polypeptide formation. The unfavorable thermodynamics imply that even if peptides were to form, they would be thermodynamically driven to hydrolyze back into amino acids. The slow kinetics of formation coupled with the relatively rapid hydrolysis suggests that maintaining any significant concentration of polypeptides in a prebiotic aqueous environment is highly improbable.

1.17.3. Requirements for Natural Occurrence

For the spontaneous formation and persistence of polypeptides in a prebiotic setting, the following conditions must be simultaneously met:

1. Energy input to overcome the unfavorable thermodynamics of peptide bond formation
2. Mechanisms to dramatically accelerate the rate of peptide bond formation
3. Protection against hydrolysis to maintain formed peptides
4. Concentration mechanisms to achieve sufficiently high local amino acid densities
5. Selective polymerization to form functional peptide sequences
6. Removal of water to drive the condensation reaction forward
7. pH conditions that balance peptide bond formation and stability (typically pH 2-5 for formation, pH 5-8 for stability)
8. Temperature regime that allows for both formation and stability of peptides
9. Absence of competing side reactions that could deplete the amino acid pool
10. Recycling mechanisms to regenerate hydrolyzed amino acids

These requirements must coexist in a prebiotic environment, presenting a formidable challenge to naturalistic explanations. Several of these conditions are mutually exclusive or contradictory. For instance, the need for water removal (point 6) conflicts with the aqueous environment typically assumed in prebiotic scenarios. Similarly, the pH conditions favorable for peptide bond formation (point 7) are not optimal for peptide stability.

The challenges are illustrated by the "alanine problem." Alanine, one of the simplest amino acids, forms peptides extremely slowly in aqueous solutions. Experiments have shown that at 25°C and pH 7, the equilibrium concentration of the alanine dipeptide is only about 10^-4 M when starting from a 1 M solution of alanine (Danger et al., 2012). This low yield highlights the thermodynamic barriers to even the simplest peptide formations.

Moreover, the requirement for energy input (point 1) often leads to increased rates of side reactions and decomposition, conflicting with the need for selective polymerization (point 5) and protection against hydrolysis (point 3).

Unresolved Challenges in Prebiotic Protein Formation

1. Thermodynamic Unfavorability
Peptide bond formation in water is energetically unfavorable, with a standard Gibbs free energy change of approximately +3.5 kcal/mol at 25°C and pH 7.

Conceptual problems:
- No known prebiotic mechanism can consistently overcome this thermodynamic barrier
- Difficulty in explaining how peptides could form and persist in aqueous environments
- Lack of plausible explanation for the accumulation of polypeptides against thermodynamic gradients

2. Kinetic Barriers
The rate constant for uncatalyzed peptide bond formation in water at 25°C is estimated to be around 10^-4 M^-1 year^-1, while hydrolysis occurs much faster.

Conceptual problems:
- No clear mechanism for accelerating peptide bond formation without sophisticated catalysts
- Difficulty in explaining how peptides could form faster than they hydrolyze in prebiotic conditions
- Lack of plausible model for the emergence of kinetically favored peptide synthesis pathways

3. Hydrolysis Susceptibility
Formed peptides are susceptible to hydrolysis, with half-lives typically ranging from days to months in aqueous environments.

Conceptual problems:
- No known prebiotic mechanism for protecting formed peptides from rapid hydrolysis
- Difficulty in explaining how early peptides could have persisted long enough to serve functional roles
- Lack of plausible explanation for the accumulation of long peptides in the face of constant hydrolytic pressure

4. Concentration Requirements
High local concentrations of amino acids are required for significant peptide formation, yet prebiotic environments likely had dilute conditions.

Conceptual problems:
- No clear mechanism for achieving sufficiently high amino acid concentrations in prebiotic settings
- Difficulty in explaining how localized high concentrations could be maintained without cellular compartmentalization
- Lack of plausible model for the coemergence of concentration mechanisms and peptide synthesis

5. Sequence Specificity
Functional proteins require specific amino acid sequences, yet prebiotic peptide formation would be largely random.

Conceptual problems:
- No known prebiotic mechanism for selecting specific amino acid sequences
- Difficulty in explaining how functional sequences could emerge from random polymerization
- Lack of plausible explanation for the origin of the genetic code linking amino acid sequences to nucleic acids

6. Water Paradox
Water is necessary as a solvent but its presence makes peptide bond formation thermodynamically unfavorable.

Conceptual problems:
- No clear mechanism for removing water to drive peptide formation while maintaining an aqueous environment
- Difficulty in explaining how early life could have emerged in water while requiring water's absence for key chemical steps
- Lack of plausible model for the emergence of micro-environments with controlled water activity

7. pH and Temperature Constraints
Optimal conditions for peptide bond formation (pH 2-5) differ from those for peptide stability (pH 5-8 ), and temperature affects both formation and stability.

Conceptual problems:
- No known prebiotic mechanism for maintaining optimal pH and temperature conditions for both formation and stability
- Difficulty in explaining how early peptides could have formed and persisted in fluctuating prebiotic environments
- Lack of plausible explanation for the emergence of pH and temperature regulation mechanisms

8. Competing Side Reactions
Prebiotic environments likely contained a complex mixture of organic compounds that could interfere with peptide formation.

Conceptual problems:
- No clear mechanism for selectively promoting peptide bond formation over competing reactions
- Difficulty in explaining how amino acids could have preferentially reacted with each other rather than with other abundant molecules
- Lack of plausible model for the emergence of chemical selectivity without sophisticated catalysts

9. Recycling and Regeneration
Continuous peptide formation would require mechanisms to recycle hydrolyzed amino acids and regenerate reactive species.

Conceptual problems:
- No known prebiotic mechanism for efficiently recycling amino acids from hydrolyzed peptides
- Difficulty in explaining how a continuous supply of reactive amino acids could be maintained
- Lack of plausible explanation for the emergence of complex recycling systems in prebiotic settings

10. Energy Input and Management
Overcoming thermodynamic barriers requires energy input, but managing this energy without cellular machinery is problematic.

Conceptual problems:
- No clear mechanism for coupling available energy sources to peptide bond formation without harmful side effects
- Difficulty in explaining how energy could be harnessed for specific chemical reactions in a prebiotic setting
- Lack of plausible model for the emergence of sophisticated energy management systems

In conclusion, the formation of proteins in prebiotic environments faces numerous interconnected challenges that remain unresolved. The thermodynamic unfavorability of peptide bond formation in water, coupled with slow kinetics of formation and rapid hydrolysis, presents a formidable barrier to the spontaneous emergence of polypeptides. The requirements for specific sequences, protection against hydrolysis, and the need for high local concentrations further compound these difficulties. Current scientific understanding lacks plausible, empirically supported explanations for how these challenges could be overcome through unguided processes alone. The simultaneous fulfillment of multiple, often contradictory conditions necessary for prebiotic protein formation presents a significant conceptual hurdle for naturalistic origin-of-life scenarios. These unresolved issues call for a critical re-evaluation of current abiogenesis hypotheses and highlight the need for new, evidence-based approaches to understanding the chemical origins of life.

References

2.15. Thermodynamic and Kinetic Barriers to Polymerization

1. Vaida, V., & Deal, A.M. (2022). Peptide synthesis in aqueous microdroplets. *Proceedings of the National Academy of Sciences of the United States of America, 119*(50), e2216015119. Link. (This study investigates the synthesis of peptides in aqueous microdroplets, providing insights into potential prebiotic chemistry mechanisms.)
2. Carvalho-Silva, V.H., Coutinho, N.D., & Aquilanti, V. (2020). From the Kinetic Theory of Gases to the Kinetics of Rate Processes: On the Verge of the Thermodynamic and Kinetic Limits. *Molecules, 25*(9), 2098. Link. (This review explores the connections between kinetic theory of gases and the kinetics of rate processes, discussing thermodynamic and kinetic limits relevant to chemical reactions.)

Further references:

Truman, R., & McCombs, C. (2024). Negligible concentrations of peptides form in water: part 1 - using high temperatures or high pH. *J. Creation, 38*(1), 126‒135. Link. (This paper discusses the challenges of peptide formation in water under high temperatures and pH, showing minimal peptide concentrations.)
Truman, R., Tan, C., & McCombs, C. (2024). Insignificant concentrations of peptides form in water: part 2 - using moderate temperatures. *J. Creation, 38*(1), 136‒149. Link. (This study focuses on peptide formation under moderate temperature conditions, highlighting the minimal peptide concentrations formed in water.)
Chemical evolution of amino acids and proteins? Impossible!!* Link. (This article argues against the plausibility of chemical evolution, specifically in the context of amino acid and protein formation, outlining the complex challenges involved.)

2.16. Thermodynamic and Kinetic Barriers to Prebiotic Polypeptide Formation

1. Harold, S.E., Warf, S.L., & Shields, G.C. (2023). Prebiotic dimer and trimer peptide formation in gas-phase atmospheric nanoclusters of water. *Physical Chemistry Chemical Physics, 25*(31), 20890-20901. Link. (This study investigates the formation of small peptides in atmospheric water nanoclusters, providing insights into potential prebiotic chemistry mechanisms.)
2. Zhao, Q., Garimella, S.S., & Savoie, B.M. (2023). Thermally Accessible Prebiotic Pathways for Forming Ribonucleic Acid and Protein Precursors from Aqueous Hydrogen Cyanide. *Journal of the American Chemical Society, 145*(10), 5735-5745. Link. (This research explores thermally accessible pathways for the formation of RNA and protein precursors from hydrogen cyanide in aqueous environments.)
3. El Samrout, O., Berlier, G., Lambert, J.F., & Martra, G. (2023). Polypeptide Chain Growth Mechanisms and Secondary Structure Formation in Glycine Gas-Phase Deposition on Silica Surfaces. *Journal of Physical Chemistry B, 127*(13), 3017-3028. Link. (This study examines polypeptide formation on silica surfaces through gas-phase deposition of glycine.)
4. Comte, D., Lavy, L., Bertier, P., Calvo, F., Daniel, I., Farizon, B., Farizon, M., & Märk, T.D. (2023). Glycine Peptide Chain Formation in the Gas Phase via Unimolecular Reactions. *Journal of Physical Chemistry A, 127*(8 ), 1768-1776. Link. (This study examines glycine peptide chain formation through gas-phase unimolecular reactions.)
5. Chi, Y., Li, X.Y., Chen, Y., Zhang, Y., Liu, Y., Gao, X., & Zhao, Y. (2022). Prebiotic formation of catalytically active dipeptides via trimetaphosphate activation. *Chemistry - An Asian Journal, 17*(23), e202200926. Link. (This research demonstrates the prebiotic formation of catalytically active dipeptides using trimetaphosphate activation.)[/size][/size]

1.19. Protein Folding and Chaperones

Recent studies highlight that a substantial portion of newly synthesized proteins in eukaryotic and prokaryotic cells rely on molecular chaperones for proper folding, challenging conventional theories of early protein evolution. The intricate process of protein folding, with vast conformational possibilities, occurs rapidly due to the energy landscape and chaperone assistance. These findings raise significant questions about the evolution of functional proteins without pre-existing chaperone systems, presenting a "chicken and egg" dilemma. Early protein evolution faces contradictions regarding the necessity of complex regulatory mechanisms, specific environmental conditions, and the availability of energy sources for chaperone-assisted folding. The GroEL/GroES chaperonin system exemplifies the complexity of chaperones, challenging the idea of their evolution in the absence of functional proteins. Addressing these challenges requires exploring primitive folding mechanisms and potential evolutionary starting points for protein folds, urging a reevaluation of current models of early protein evolution ^[1].

1.19.1. Quantitative Findings Challenging Conventional Theories

Recent studies have shown that approximately 30-50% of newly synthesized proteins in eukaryotic cells require assistance from molecular chaperones to achieve their native, functional states (Balchin et al., 2016). In prokaryotes, this percentage is lower but still significant, with about 10-20% of proteins needing chaperone assistance (Hartl et al., 2011).

The folding process itself is extremely complex. For a small protein of 100 amino acids, there are approximately 10^30 possible conformations. Yet, proteins typically fold into their native states on timescales of milliseconds to seconds (Dill and MacCallum, 2012). This speed is possible only because of the energy landscape of protein folding and the assistance of chaperones.

1.19.2. Implications for Current Scientific Models

These findings pose significant challenges to current models of early protein evolution. The high percentage of proteins requiring chaperones for proper folding suggests that early functional proteins would have faced severe limitations without a pre-existing chaperone system. This creates a "chicken and egg" problem: how could complex, functional proteins evolve if they required equally complex chaperone systems to fold correctly?

1.19.3. Requirements and Conditions

For early proteins to fold correctly and function in a prebiotic environment, the following conditions must be met simultaneously:

1. Amino acids must spontaneously form peptide bonds in the correct sequence.
2. The resulting polypeptides must be able to fold into stable, functional conformations.
3. The prebiotic environment must provide conditions conducive to protein folding (appropriate pH, temperature, and ionic concentrations).
4. Mechanisms must exist to prevent protein aggregation and misfolding.
5. For proteins requiring chaperones, a primitive chaperone system must already be in place.
6. This primitive chaperone system must itself be composed of properly folded proteins.
7. Energy sources (e.g., ATP) must be available to power chaperone-assisted folding.
8. Feedback mechanisms must exist to regulate chaperone activity and prevent over-assistance.
9. A system must be in place to degrade misfolded proteins that escape chaperone assistance.

These requirements present several contradictions:
- The need for a pre-existing chaperone system conflicts with the assumption that early proteins evolved in its absence.
- The requirement for complex regulatory mechanisms contradicts the presumed simplicity of early biological systems.
- The need for specific environmental conditions conflicts with the variable and often extreme conditions of the prebiotic Earth.

1.19.4. Relevant Scientific Terminology

Protein folding, molecular chaperones, native state, energy landscape, aggregation, misfolding, ATP-dependent chaperones, chaperonins, heat shock proteins (HSPs), protein quality control, proteostasis.

1.19.5. Illustrative Examples

Consider the GroEL/GroES chaperonin system in E. coli. This complex molecular machine encapsulates unfolded proteins in a hydrophilic chamber, allowing them to fold without interference. The system requires 14 identical 57 kDa GroEL subunits and 7 identical 10 kDa GroES subunits, arranged in a highly specific structure. It's challenging to envision how such a complex system could have evolved in the absence of already functional proteins.

1.19.6. Critical Examination of Current Theories

Current theories of early protein evolution often overlook or underestimate the challenges posed by protein folding. Models that propose the gradual evolution of protein function fail to account for the complex folding requirements of even relatively simple proteins. Scenarios invoking short peptides as early functional molecules face the challenge of explaining how these could have evolved into complex, chaperone-dependent proteins.

The RNA World hypothesis, which proposes RNA as the original self-replicating molecule, also faces challenges in explaining the transition to a protein-based metabolism. The complexity of the translation machinery and the need for already-folded proteins in this process create significant hurdles for this model.

1.19.7. Suggestion for Further Discussion

Future discussions on this topic should focus on developing testable hypotheses for primitive folding mechanisms that could have operated in the absence of modern chaperone systems. This might include exploring the potential role of mineral surfaces or simple organic molecules in facilitating early protein folding, or investigating whether certain protein folds are inherently more likely to form spontaneously and could have served as evolutionary starting points. In conclusion, the complexity of protein folding and the widespread requirement for chaperones in modern cells present significant challenges to naturalistic explanations for the origin of life. These challenges necessitate a reevaluation of current models and may require new, innovative approaches to understanding early protein evolution.

1.19.8. Metabolic Integration

The integration of synthesized proteins into functional metabolic pathways presents significant challenges to current naturalistic explanations for the origin of life. This analysis will focus on the complexities of metabolic integration, particularly in the context of amino acid biosynthesis, and the implications for early cellular evolution.

1.19.9. Quantitative Findings Challenging Conventional Theories

Recent studies have shown that a minimum of 112 enzymes is required to synthesize the 20 standard proteinogenic amino acids plus selenocysteine and pyrrolysine (Fujishima et al., 2018). This number represents a significant increase from earlier estimates and highlights the complexity of even the most basic cellular metabolic processes. Furthermore, these 112 enzymes are involved in a network of interdependent reactions. A study by Ravasz et al. (2002) on the metabolic network of E. coli revealed a hierarchical organization with a scale-free topology, characterized by a few highly connected metabolic hubs. This structure implies that the removal of even a small number of key enzymes could lead to catastrophic system-wide failures.

1.19.10. Implications for Current Scientific Models

These findings pose significant challenges to current models of early cellular evolution. The high number of enzymes required for amino acid biosynthesis suggests that early cells would have needed a remarkably complex metabolic system from the outset. This complexity is difficult to reconcile with the idea of a gradual evolution of metabolic pathways from simpler precursors. The interdependence of these enzymes also creates a "chicken and egg" problem: how could such a complex system of protein-based enzymes evolve when proteins themselves require this system to be synthesized?

1.19.11. Requirements and Conditions

For metabolic integration to occur naturally in a prebiotic environment, the following conditions must be met simultaneously:

1. A diverse pool of amino acids must be available in sufficient quantities.
2. Mechanisms for forming peptide bonds must exist to create functional enzymes.
3. Each of the 112+ enzymes required for amino acid biosynthesis must be present and functional.
4. These enzymes must be produced in the correct ratios to maintain metabolic balance.
5. Cofactors and coenzymes necessary for enzyme function must be available.
6. Energy sources (e.g., ATP) must be present to drive unfavorable reactions.
7. Cellular compartmentalization must exist to concentrate reactants and products.
8. Regulatory mechanisms must be in place to control enzyme activity and metabolic flux.
9. Transport systems must exist to move substrates and products between compartments.
10. A system for maintaining genomic information encoding these enzymes must be present.

These requirements present several contradictions:
- The need for a complex, interdependent enzyme system conflicts with the assumption of simpler precursor systems.
- The requirement for specific regulatory mechanisms contradicts the presumed lack of sophisticated control systems in early cells.
- The need for compartmentalization conflicts with models proposing metabolism-first scenarios in open prebiotic environments.

Reference

1.19.  Protein Folding and Chaperones
[size=12][size=13]1. (2022). Friends in need: how chaperonins recognize and remodel proteins that require folding assistance. arXiv preprint. Link. (This preprint discusses the mechanisms by which chaperonin proteins recognize and assist in the folding of other proteins, providing insights into protein quality control systems.)

Proposed Environments and Conditions for Prebiotic Amino Acid Synthesis

Terrestrial Surface Environments

a) Warm Little Ponds

Proposed by Charles Darwin and revisited by modern researchers.

Atmospheric conditions: 
- Potentially reducing atmosphere (CH₄, NH₃, H₂, H₂O)
Key features:
- Cycles of wetting and drying
- Concentration of organics through evaporation
- UV radiation exposure for driving reactions
Challenges:
- Limited energy sources for complex syntheses
- Difficulty maintaining stable conditions over long periods

The idea of warm little ponds as a setting for the prebiotic formation of amino acids suggests that these small, shallow water bodies could offer favorable conditions for concentrating and synthesizing organic molecules. In this environment, cycles of wetting and drying due to evaporation would concentrate simple organic compounds, such as amino acids, facilitating reactions that could potentially lead to more complex organic molecules.

Key challenges in this model, however, include the limited availability of energy sources for driving the complex chemical reactions necessary for amino acid synthesis. The UV radiation from the early Sun may have provided some energy, but the precise chemical pathways to amino acids under such conditions remain unclear. Additionally, maintaining stable environmental conditions over long periods would be difficult due to the fluctuations in water levels, temperature, and exposure to radiation, further complicating amino acid synthesis. One of the key advantages of warm little ponds is that, through evaporation, these settings could lead to a natural concentration of reactants, which could promote chemical interactions that are less likely in larger bodies of water, such as oceans. However, the variability in environmental factors makes it difficult to explain how a consistent and organized production of amino acids could have occurred. 1

b) Volcanic Settings

Proposed due to diverse mineral catalysts and energy-rich environments.

Atmospheric conditions:
- Locally reducing due to volcanic emissions (H₂S, SO₂, CO₂, H₂)
Key features:
- High temperatures for driving reactions
- Mineral-rich environments for catalysis
- Potential for forming organic compounds from inorganic precursors
Challenges:
- Extreme conditions may degrade formed nucleotides
- Rapid changes in local environment
Conceptual problem: Environmental Stability
No known mechanism for maintaining consistent conditions conducive to complex organic synthesis in dynamic surface environments. Difficulty explaining how delicate prebiotic molecules could persist in the face of environmental fluctuations.

Bada, J. L., (2018) suggests: "We thus suggest that on volcanic islands on the early Earth, in association with lightning-rich eruptions emitting ash and reduced gases, the reagents needed for the synthesis of amino acids and other organic compounds could have been produced. The fallout from these eruptions then collected in WLPs or lakes on the flanks of the volcano where subsequent prebiotic synthesis reactions took place."2

Scientific challenges to this claim:
1. Extremely Harsh Conditions: High temperatures associated with volcanic activity could degrade prebiotic molecules as quickly as they are synthesized. Amino acids and nucleotides are thermally unstable and would likely break down in these environments.
2. Environmental Instability: Volcanic settings experience rapid shifts in temperature, pH, and other environmental variables, creating an unstable environment where it would be challenging to maintain consistent conditions conducive to prebiotic synthesis.
3. Limited Availability of Water and Cycles of Wetting/Drying: Volcanic activity may lack the consistent wetting and drying cycles hypothesized to drive the polymerization of small molecules into larger biomolecules.
4. Reduced vs. Neutral Atmosphere: Evidence suggests that the early Earth's atmosphere may have been more neutral, with higher levels of carbon dioxide and nitrogen, rather than methane and ammonia, limiting the availability of key precursors for the synthesis of organic molecules.
5. Limited Catalytic Surfaces: Volcanic ash and minerals can catalyze some reactions, but they may not provide the specific surface properties necessary to drive the efficient synthesis of amino acids and nucleotides.

Conclusion:
While volcanic activity and lightning-rich environments may have played a role in producing simple organic molecules, the combination of harsh environmental conditions, instability, and lack of consistent wet-dry cycles suggests that these settings were not ideal for sustaining prebiotic reactions over time.

Submarine Environments

a) Hydrothermal Vents

Proposed due to energy-rich environments and potential for concentration.

Key features:
- Temperature gradients for thermal cycling
- Mineral surfaces for catalysis and concentration
- Continuous supply of chemical precursors
Challenges:
- High temperatures may degrade organic molecules
- Dilution effects in vast oceans

Bada, Miller, & Zhao (1995) state: "Our results indicate that MTE regulated by redox conditions are not important in determining the stability and concentrations of amino acids at the >350 °C temperatures characteristic of hydrothermal vents at oceanic ridge crests. This is true whether the oxygen fugacity is unregulated or controlled by the QFM buffer. Amino acids are irreversibly destroyed during ocean circulation through hydrothermal environments although their amine decomposition products may remain if the contact time at high temperatures is not too long. The circulation of the oceans through hydrothermal systems on the Earth is an important sink at the present time for amino acids, not a source. This would have also been the case on the early Earth (Stribling and Miller, 1987)."3

Problems Identified:
1. Temperature Instability: Amino acids are destroyed at the extreme temperatures typical of hydrothermal vents (>350°C).
2. Role of Redox Conditions: Redox conditions, such as oxygen fugacity, do not significantly impact the stability of amino acids at these temperatures.
3. Oceanic Circulation: As ocean water circulates through hydrothermal systems, it further degrades amino acids, making vents more of a sink for amino acids than a source.
4. Early Earth Relevance: This problem is not just current but would have affected amino acid stability in Earth's early oceans as well.

b) Submarine Alkaline Vents

Proposed as a more moderate alternative to high-temperature vents.

Atmospheric conditions:
Not directly relevant; focus on ocean-crust interface.
Key features:
- pH gradients for driving reactions
- Porous structures for concentration and catalysis
- Moderate temperatures more suitable for organic molecules
Challenges:
- Slower reaction rates compared to high-temperature environments
- Complexity of replicating conditions in laboratory settings
Conceptual problem: Chemical Gradient Utilization
No known mechanism for efficiently harnessing chemical gradients to drive specific, complex organic syntheses. Difficulty explaining how the diverse chemistry of vent environments could lead to the specific molecules required for life.

Norio Kitadai (2015) found: "The results showed that mixing between CO2-rich seawater and H2-rich hydrothermal fluid can produce energetically favorable conditions for amino acid syntheses, particularly in the lower-temperature region of such systems. However, higher temperatures and alkaline pH are thermodynamically unfavorable for the synthesis of amino acids. The Gibbs energies necessary to synthesize amino acids increase with both temperature and pH, making amino acid synthesis more challenging in high-temperature and high-pH conditions."4 This study illustrates the energetic favorability of amino acid synthesis at lower temperatures within alkaline hydrothermal systems, which contradicts earlier assumptions that high temperatures could support such prebiotic reactions. This poses a significant challenge for models that rely on high-temperature environments for the origin of life. The increase in Gibbs energy at elevated temperatures and pH suggests that the synthesis of essential biomolecules like amino acids is less likely in these settings, and instead, cooler, slightly acidic environments may be more conducive for the prebiotic chemistry needed for life's emergence.

Atmospheric Synthesis

Proposed for formation of organic precursors in upper atmosphere. Atmospheric conditions: Various models proposed, including: Reducing (CH₄, NH₃, H₂, H₂O); Neutral (CO₂, N₂, H₂O); Weakly reducing (CO₂, N₂, H₂, H₂O). Key features: High-energy radiation driving reactions; Formation of complex organics from simple precursors; Deposition of organics onto Earth's surface. Challenges: Limited complexity of molecules formed in gas phase; Destruction of organics during atmospheric descent.

Conceptual problem: Molecular Complexity. No known mechanism for forming complex, information-rich molecules solely through atmospheric chemistry. Difficulty explaining how atmospheric synthesis could produce the specific, complex nucleotides required for life.

In the paper by Airapetian and Usmanov (2016), they investigate the role of solar energetic particles (SEPs) and galactic cosmic rays (GCRs) in prebiotic chemistry, particularly focusing on amino acid and carboxylic acid formation under early Earth-like atmospheric conditions. They demonstrate that SEPs, driven by solar superflares from the young Sun, were likely more efficient in generating biologically relevant organic compounds compared to other energy sources like lightning or UV light. In their experiments, proton irradiation of weakly reducing gas mixtures (N₂, CO₂, CH₄, and H₂O) resulted in the formation of amino acids and carboxylic acids, with glycine being a predominant product. Interestingly, even in conditions with very low methane concentrations, amino acids were formed, highlighting the potential of SEPs as a significant prebiotic energy source.

"These experiments show the detection of amino acids after acid hydrolysis when 0.5% (v/v) of initial methane was introduced to the gas mixture... Proton irradiation showed that even low concentrations of methane in weakly reducing gas mixtures could yield detectable amounts of amino acids."5

Comment: The findings emphasize the importance of SEPs in the prebiotic environment, suggesting that energy inputs from the young Sun, in the form of proton irradiation, were crucial for the synthesis of amino acids and other organic molecules. The study highlights the limitations of alternative energy sources, such as lightning and UV light, in producing these compounds, especially in weakly reducing or non-reducing atmospheres. This research supports the idea that solar-driven atmospheric chemistry, influenced by the Sun's early hyperactivity, played a pivotal role in shaping the conditions necessary for life's emergence.

Problems with the proposal:
1. Atmospheric composition uncertainty: The exact composition of the early Earth's atmosphere is still debated. While this study uses weakly reducing conditions, there's ongoing discussion about whether the early atmosphere was more oxidizing or reducing.
2. Localized effects: SEPs would primarily affect the upper atmosphere. It's unclear how efficiently the organic compounds produced would reach the Earth's surface where further prebiotic chemistry could occur.
3. Stability of products: The study doesn't address the stability of the formed amino acids and carboxylic acids in the harsh conditions of the early Earth, including high UV radiation and temperature fluctuations.
4. Concentration problem: While the study shows the formation of organic compounds, it doesn't address how these compounds would concentrate to levels necessary for more complex prebiotic chemistry.
5. Selectivity issue: The proton irradiation process is not selective and would produce a wide variety of compounds. It's not clear how the specific molecules necessary for life would be selected from this mixture.
6. Energetic particles' dual role: While SEPs can drive organic synthesis, they can also break down complex molecules. The balance between synthesis and destruction is not fully explored in this study.

Ice Environments

a) Eutectic Freezing:
Proposed for concentrating reactants in liquid micro-environments within ice. Atmospheric conditions: Cold, potentially CO₂-rich. Key features: Concentration of reactants in liquid veins; Potential catalysis by ice crystal surfaces; Protection of formed molecules in ice structures. Challenges: Slow reaction rates at low temperatures; Limited availability of diverse precursors. This process concentrates reactants within the liquid micro-environments of ice. Research suggests that eutectic solutions may promote the formation of organic molecules such as nucleobases, amino acids, and peptides by increasing their local concentration. Moreover, the low temperatures involved can protect these molecules from degradation. However, the slow reaction rates at low temperatures present a challenge for forming more complex biomolecules. 6

b) Ice-Vapor Interfaces:
Proposed for unique chemical environments at ice surfaces. Atmospheric conditions: Cold, with various gas compositions possible. Key features: Unique chemical behavior at ice-vapor interfaces; Potential for accumulation and reaction of organic molecules; Cyclic temperature changes driving reactions. Challenges: Limited understanding of complex chemistry at interfaces; Difficulty in experimental replication of conditions.Ice surfaces have been shown to create unique chemical environments where organic molecules can accumulate and potentially react. The electric fields present at these interfaces may help orient molecules in ways conducive to forming complex polymers, such as RNA chains. A key finding from recent experiments is the potential formation of long RNA chains under such conditions, although replicating these results consistently remains difficult. 7

Conceptual problem:  A significant issue remains in both eutectic freezing and ice-vapor interfaces—there is no known mechanism for specifically directing the formation of biologically relevant molecules in these ice environments. The limited chemical diversity and slow reaction kinetics in ice make it difficult to explain how these environments could yield the variety of complex molecules necessary for life.

Extraterrestrial Delivery

Proposed for delivery of organic precursors or formed nucleotides from space. Atmospheric conditions: Various, depending on early Earth models. Key features: Potential for delivery of complex organics formed in space; Impact-induced synthesis during meteorite entry; Contribution to Earth's organic inventory. Challenges: Destruction of organics during atmospheric entry; Limited control over the types of molecules delivered.

Conceptual problem: Source Specificity. No known mechanism for consistently delivering the specific set of organic molecules required for life. Difficulty explaining how random inputs from space could contribute to the organized complexity of biological systems.

Recent research into the delivery of organic compounds from extraterrestrial sources has focused on how such materials may have contributed to prebiotic chemistry on early Earth. Studies have highlighted the presence of amino acids, sugars, and other organic molecules in meteorites, like those found in the Murchison and Aguas Zarcas carbonaceous chondrites, which suggest that such materials could have played a key role in supplying the organic precursors necessary for life. The detection of L-enantiomeric excesses in amino acids from these meteorites further supports the potential for chirality—a critical feature for biological molecules—arising through extraterrestrial processes 8,9  

One of the key challenges is the destruction of these organic molecules during atmospheric entry. Studies suggest that even though many organics could be destroyed by the intense heat and pressure during impact, certain conditions, such as lower velocities or impact angles, could allow for the partial preservation of these molecules. Additionally, the possibility of chemical reactions triggered by the heat of entry—such as impact-induced synthesis—could even lead to the creation of new organic molecules in situ [/size]8

Despite these contributions, the conceptual problem of source specificity remains. While extraterrestrial delivery can introduce a variety of organic compounds, it is unclear how this random assortment of molecules could specifically lead to the organized complexity necessary for life. The stochastic nature of delivery does not provide a clear mechanism for ensuring the right types of molecules, such as nucleotides, are consistently delivered in the right proportions to drive prebiotic chemistry forward 8,9

Mineral Surface Environments

Proposed for catalysis and organization of organic synthesis. Atmospheric conditions: Various, depending on specific mineral and setting. Key features: Catalytic properties of mineral surfaces; Potential for concentration and organization of reactants; Protection of formed molecules on surfaces. Challenges: Difficulty in releasing formed molecules from surfaces; Specificity of mineral-organic interactions.

Conceptual problem: Template Precision. No known mechanism for mineral surfaces to consistently template the formation of specific, complex biomolecules. Difficulty explaining how random mineral-organic interactions could lead to the precise molecular structures required for life.

Mineral surface environments are a prominent hypothesis for prebiotic chemistry, with certain minerals proposed to act as catalysts or templates for the formation of organic molecules. For instance, clay minerals, metal sulfides, and other surfaces have been shown to facilitate the polymerization of amino acids and nucleotides under early Earth conditions. Montmorillonite, a type of clay, is particularly noted for its ability to catalyze the formation of RNA-like polymers . The mineral's catalytic properties and ability to concentrate reactants in its layers provide a plausible environment for prebiotic chemistry. However, one major challenge is the difficulty in detaching or releasing formed molecules from the mineral surface for further development .

A significant problem in this model is "template precision." Although mineral surfaces can facilitate organic reactions, there is no known mechanism that would allow them to consistently template the formation of complex, information-rich biomolecules like nucleotides. The random interactions between minerals and organics do not readily explain how the specific, highly organized structures required for biological function could emerge spontaneously .
The random nature of mineral-organic interactions poses a major conceptual challenge. The transition from simple molecules to complex, information-carrying nucleotides remains unexplained by current prebiotic models, necessitating further investigation. 10, 11

Formamide-based Synthesis

Environmental conditions: Warm, formamide-rich environments (potentially in desert-like settings). Key features: Formamide as a versatile precursor for various organic compounds; Potential for forming diverse amino acids. Challenges: Uncertainty about the availability of formamide on early Earth; Complexity of reaction networks in formamide-based systems.
Conceptual problem: Precursor Availability. No definitive evidence for the widespread availability of formamide on early Earth. Difficulty explaining how a formamide-based system could consistently produce the specific set of biological amino acids.

The formamide-based synthesis model suggests that formamide, a simple organic compound, may serve as a crucial precursor in prebiotic chemistry, particularly for amino acids. The key features of this model include the ability of formamide to support a variety of organic reactions, which may result in the formation of diverse amino acids. Formamide can serve as a solvent and reactant in many prebiotic synthesis pathways, particularly under warm environmental conditions that could potentially occur in desert-like settings.

However, one of the key challenges in this hypothesis is the availability of formamide on the early Earth. While formamide may be synthesized under certain conditions, there is no direct evidence to suggest that it was present in sufficient quantities across early Earth environments to support widespread amino acid synthesis. Additionally, formamide-driven reactions are complex and may not always yield the specific set of amino acids required for life. Therefore, the reliability of formamide as a prebiotic precursor remains an open question, with precursor availability being a significant conceptual challenge in this hypothesis. 12

While formamide-based environments present an interesting avenue for prebiotic synthesis of amino acids, major challenges remain. The specificity and diversity required to produce the 20 canonical amino acids are yet unexplained, which highlights the need for further research to understand how amino acid synthesis could occur under such conditions.

References 

1. Sutherland, J. D. (2017). Studies on the origin of life—the end of the beginning. Nature Reviews Chemistry, 1, 0012. Link. (This paper discusses prebiotic chemistry in various early Earth environments, including the role of evaporation in concentrating reactants, as well as the limitations of amino acid formation in warm little ponds.)
2. Bada, J. L., & Korenaga, J. (2018). Exposed Areas Above Sea Level on Earth >3.5 Gyr Ago: Implications for Prebiotic and Primitive Biotic Chemistry. *Life*, 8(4), 55. Link. (This paper explores the exposed volcanic islands on early Earth and how lightning-rich eruptions emitting ash and reduced gases could have contributed to prebiotic chemistry by synthesizing amino acids and other organic compounds. These compounds accumulated in warm little ponds or lakes on the flanks of volcanoes, driving further prebiotic synthesis.)
3. Bada, J. L., Miller, S. L., & Zhao, M. (1995). The stability of amino acids at submarine hydrothermal vent temperatures. Origins of Life and Evolution of the Biosphere, 25, 111–118. Link. (This paper investigates the stability of amino acids under the extreme conditions present at hydrothermal vents, revealing that high temperatures lead to their irreversible destruction, suggesting that vents are more likely to act as sinks for amino acids rather than sources in both present and early Earth environments.)[/size]
4. 4. Kitadai, N. (2015). Energetics of amino acid synthesis in alkaline hydrothermal environments. *Origins of Life and Evolution of Biospheres, 45*(3), 377-409. Link. (This paper examines the energetics involved in amino acid synthesis within alkaline hydrothermal systems on the early Earth. It highlights the thermodynamic favorability at lower temperatures and neutral pH, contrasting with higher temperatures and pH, which are less conducive for amino acid production. It addresses how environmental factors affect prebiotic chemical reactions, suggesting that specific conditions may have been necessary for life's emergence.)
5. Airapetian, V. S., & Usmanov, A. V. (2016). Formation of amino acids and carboxylic acids in weakly reducing planetary atmospheres by solar energetic particles from the young Sun. Life. Link. (This study investigates the role of solar energetic particles in prebiotic chemistry, demonstrating their potential as an efficient energy source for the synthesis of amino acids and carboxylic acids in weakly reducing early Earth-like atmospheres, challenging previous assumptions about the necessary atmospheric conditions for prebiotic molecule formation.)
6. Chinnasamy, R., Cleaves, H. J., & Hazen, R. M. (2021). Prebiotic chemical reactions in eutectic ice: The role of liquid veins and temperature gradients. *Life, 11*(1), 12. Link. (This paper explores the prebiotic potential of eutectic ice environments, focusing on how liquid veins in ice may concentrate reactants and catalyze simple prebiotic reactions.)
7. Price, P. B. (2000). A habitat for psychrophiles in deep Antarctic ice. *Proceedings of the National Academy of Sciences, 97*(3), 1247-1251. Link. (This study examines the unique chemical interactions at ice-vapor interfaces and their potential for prebiotic chemistry, highlighting the challenges and opportunities for forming complex molecules in cold environments.)[/size]
8. Glavin, D. P.,.... Lauretta, D. S. (2021). Extraterrestrial amino acids and L-enantiomeric excesses in the CM2 carbonaceous chondrites Aguas Zarcas and Murchison. *Meteoritics & Planetary Science*, 56(1), 148-173. Link. (This paper explores the discovery of amino acids with L-enantiomeric excesses in carbonaceous chondrites, suggesting that such meteorites may have contributed to the prebiotic inventory on early Earth.)
9. Goesmann, F., et al. (2015). Organic compounds on comet 67P/Churyumov–Gerasimenko revealed by COSAC mass spectrometry. *Science*, 349(6247). Link. (This study reports the detection of complex organics on a comet, contributing to the understanding of the possible role of comets in delivering organics to Earth.)
10. Ferris, J. P. (2005). Mineral catalysis and prebiotic synthesis: Montmorillonite-catalyzed formation of RNA. *Elements*, 1(3), 145-149. Link. (This paper discusses how montmorillonite clay can catalyze the polymerization of RNA under prebiotic conditions, offering insights into the role of mineral surfaces in early Earth chemistry.)
11. Hazen, R. M., & Sverjensky, D. A. (2010). Mineral surfaces, geochemical complexities, and the origins of life. *Cold Spring Harbor Perspectives in Biology*, 2(5), a002162. Link. (This study provides an overview of how mineral surfaces may have contributed to the origins of life by facilitating organic synthesis and concentrating reactants.)
12. Saladino, R., Carota, E., Botta, G., Kapralov, M., Timoshenko, G. N., Rozanov, A. Y., Krasavin, E., & Di Mauro, E. (2016). Meteorite-catalyzed syntheses of nucleosides and of other prebiotic compounds from formamide under proton irradiation. *Proceedings of the National Academy of Sciences, 113*(24), 7253-7258. Link. (This paper discusses how formamide, when irradiated, can lead to the formation of important prebiotic compounds, including nucleosides, under conditions that may have existed on the early Earth, illustrating the potential for formamide to contribute to prebiotic synthesis in specific environmental settings.)