Prebiotic Chemistry: Geochemical Context and Reaction Screening
2. Historical Factors
3. The Tempo and Timing of the Origin of Life
4. Historical Contingency and Immeasurable Variables
- The composition of the early atmosphere. While it was initially estimated that the early atmosphere was highly reducing, others have argued that it was not, and an atmosphere essentially similar to the present day one, albeit without abundant molecular oxygen was prevalent. This would affect the flux of solar radiation at various wavelengths reaching surface environments , the braking rates of impactors , as well as the flux and type of organics reaching the surface.
- The composition and properties of global and local primitive water bodies (e.g., pH, salinity, temperature), which would affect aqueous chemistry in many subtle ways (as discussed below).
- Prevailing temperatures on the prebiotic Earth’s surface, which has fundamental consequences for organic chemical processes (also discussed below).
5. Organic Chemistry as the Critical, Ahistorical Factor
- pH. A change in the pH value of the reaction environment by single pH unit can easily change reaction rates by a factor of 10. At some pH values reactions may be so inhibited, no observable reaction occurs at all. The implications for prebiotic chemistry are large, and numerous examples of dramatic pH-dependent effects exist in the literature. For example the keto-enol equilibria of the nitrogenous bases in nucleic acids, e.g., ; vesicle formation and stability , primary synthetic reactions such as the formose reaction and cyanide polymerization [68,69], and the stability of various organic compounds potentially important for the origin of life, including, but not limited to sugars , nucleobases  and small molecules such as HCN and formamide (HCONH2) .
- Concentration. Reaction rates, with few exceptions, are often proportional to reactant concentration, since the probability that two molecules will come together and react decreases as the concentration of reactants is lowered. While some multi-reactant processes may proceed in extremely dilute solution, e.g., , others are markedly slowed or do not proceed at all upon dilution, e.g., [68,72]. Concentration is also pathway-dependant; compounds must find their way by plausible processes to the environment in which they become concentrated. For example, a considerable body of work has studied the possible role of HCONH2 as a precursor to prebiotic organics. To date, reactions have not been shown to work in dilute aqueous solution, and appear to largely require temperatures above the boiling point of water . Concentration also includes two limits, a precipitation limit, beyond which compounds are insoluble, and a dilution limit, beyond which reaction is undetectable. In practice, the analytical limit of detection may be reached, but this can be overcome by various techniques. These are relatively trivial problems compared with the problem of not knowing where reactions become unproductive.
- Temperature. Most reaction rates scale as a function of temperature, according to the well-known Arrhenius equation. A typical organic transformation may increase or decrease in rate by a factor of 2 to 3 for each 10 °C change in temperature. For complex multi-component or multi-pathway reactions, these ratios may be extremely important in determining the course of reactions and their outcomes. In cases where multiple chemical steps occur simultaneously, and there are multiple reactants which are sensitive to temperature effects, the most sensitive component deserves the most careful consideration. While it may be possible to speed reactions by heating them, there may be activation barriers which produce unexpected effects at both higher and lower temperatures. As an example, recent experiments demonstrating increasing efficiency of RNA replicases have resorted to conducting reactions in ice eutectics, owing to the decreased rates of organic degradation at low temperatures . Such experiments also take advantage of the concentrating effects of ice eutectics and the stabilization of weak interactions, such as those mediated by hydrogen bonding, at low temperatures.
- Time. Lazcano and Miller observed that all known prebiotic reactions are fast . Orgel responded by pointing out that our knowledge of prebiotic chemistry may be more constrained by the lengths of post-doctoral fellowships than by any requirements of the chemistry involved . This consideration relates intrinsically to variables of concentration, pH and temperature discussed above. In some cases, it may be almost impossible to produce a laboratory reconstruction of a process for temporal reasons. Extrapolation is perfectly reasonable in such cases, with some degree of caution. To an extent, time is exchanged for temperature in prebiotic simulations. As mentioned above, it is unknown what the average or range of surface temperatures was on the primitive Earth. Micro-environments must also be considered, for example, surface temperatures on the modern Earth range from ~−90 °C to ~+60 °C.
- Pressure. Environments where pressure becomes a significant variable already make some assumptions about other relevant variables, for example temperature. The pH of ambient conditions and the pKa of reactants may change dramatically under extreme pressure conditions, and some remarkable pressure-dependant effects have been observed in prebiotic studies of peptide oligomerization, as might occur in deep marine sediments . It is interesting to speculate how difficulties of working with this parameter may skew our knowledge of abiotic organic chemistry.
- Ionic Strength. Depending on the reaction in question, this may have a relatively minor influence on chemistry, or be a significant factor. Some predictions can be made, but this is certainly worth exploring, for example in the way inorganic solute concentration may limit the ability of processes such as eutectic freezing to concentrate reactive organic solutes [78,79].
- Influence of Inorganic Reactants. Ammonia, sulfide, various transition metals, etc. can significantly affect the course of reactions. Ammonia and sulfide, depending on pH, can be significantly reactive with important prebiotic reactants . It is probably not reasonable, and possibly not productive to explore them all experimentally, and it may irrelevant to do so in some cases, however some merit at least cursory consideration where they might be expected to be relevant. For example, it is well-documented that transition metals can have significant effects on the reactivity of various compounds including amino acids and peptides [52,81]. Simple oxoanions, such as borate and silicate, have also been found to have profound effects on more complex chemistries such as sugar forming reactions [82,83,84].
- Reactant Continuity. Each reactant in any proposed scheme or reaction must fit viably with the above-mentioned considerations. For example, while glyceraldehyde may be a perfectly reasonable reactant, its derivation from a formose like process would inevitably lead to the presence of other carbohydrates and carbohydrate-like compounds [85,86]. These would, in the absence of geochemically viable purification schemes, carry over into subsequent reaction steps. As discussed below, many prebiotic processes produce extraordinarily complex mixtures, and the mere presence of a compound cannot guarantee its ability to react with a second reagent. Even novel syntheses of glyceraldehyde from other processes also result in the presence of numerous other compounds .
- Reagent Purity. In almost all known examples of prebiotic synthesis starting from primary reactants such as atmospheric gases, complex mixtures result, in which competing side reactions would be difficult to avoid. For example, in many typical primary syntheses, the yield of glycine is often quite high relative to other measured organic species, though its overall yield is rather low. Glycine represents ~0.01 wt% of the organic content of the Murchison meteorite  and is present alongside some thousands or millions of other organic molecule types . The same is true of the yield of glycine from electric discharge experiments, where despite being one of the most abundant single products, it only accounts for ~2% of the input carbon , or 0.6% of the input carbon from an aqueous HCN oligomerization reaction , in both cases again being accompanied by hundreds or thousands of other organic species (Figure 4).
- Light. The flux of solar radiation to the primitive Earths’ surface is somewhat poorly constrained, though the sun’s total luminosity was likely considerably lower . The lack of an ozone layer likely permitted much lower and more energetic wavelength radiation to reach the Earth’s surface, however trivial environmental considerations, such as protection by various dissolved inorganic species, or reactions proceeding in interstitial pore water, could have rendered such considerations essentially moot . Nevertheless, the potentially significant effects of both UV and visible light on prebiotic chemistry remain seriously understudied, underscored by the recent results of Sutherland and colleagues, among other older studies [87,93,94,95].
- Minerals. There are a great number of possible minerals which might have contributed some form of catalysis or concentration of various species . For example, iron oxide minerals have been shown to be catalysts for the both the degradation and synthesis of peptides, as well as the degradation of amino acids [51,52]. It would be unreasonable to attempt to test every possible mineral from the start, but it might be instructive to examine the effects of minerals on reactions once those reactions have been shown to work in their absence. It might be a useful exercise to consider which minerals would be likely to be common in any given environment.
- Cycling. Relatively few studies have taken into account the effects of thermal cycling. Among those that have been reported, one showed the formation of peptides in cycling hydrothermal solutions , while another showed the formation of peptides in cycling tidal environments . In both cases is was later suggested that the ultimate product yield is very close to the expected thermodynamic outcome in the absence of cycling , as may be expected for a simple reversible process, but the phenomenon likely deserves further consideration.
6. The Way Forward?
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Cleaves, H.J., II. Prebiotic Chemistry: Geochemical Context and Reaction Screening. Life 2013, 3, 331-345. https://doi.org/10.3390/life3020331
Cleaves HJ II. Prebiotic Chemistry: Geochemical Context and Reaction Screening. Life. 2013; 3(2):331-345. https://doi.org/10.3390/life3020331Chicago/Turabian Style
Cleaves, Henderson James, II. 2013. "Prebiotic Chemistry: Geochemical Context and Reaction Screening" Life 3, no. 2: 331-345. https://doi.org/10.3390/life3020331