Publications

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2016
Bada, JL, Chalmers JH, Cleaves HJ.  2016.  Is formamide a geochemically plausible prebiotic solvent? Physical Chemistry Chemical Physics. 18:20085-20090.   10.1039/c6cp03290g   AbstractWebsite

From a geochemical perspective, significant amounts of pure formamide (HCONH2) would have likely been rare on the early Earth. There may have been mixed formamide-water solutions, but even in the presence of catalyst, solutions with >= 20 weight% water in formamide would not have produced significant amounts of prebiotic compounds. It might be feasible to produce relatively pure formamide by a rare occurrence of freezing formamide/water mixtures at temperatures lower than formamide's freezing point (2.55 degrees C) but greater than the freezing point of water. Because of the high density of formamide ice it would have sunk and accumulated at the bottom of the solution. If the remaining water froze on the surface of this ice, and was then removed by a sublimation-ablation process, a small amount of pure formamide ice might have been produced. In addition a recent report suggested that similar to 85 weight% formamide could be prepared by a geochemical type of fractional distillation process, offering another possible route for prebiotic formamide production.

Raggi, L, Bada JL, Lazcano A.  2016.  On the lack of evolutionary continuity between prebiotic peptides and extant enzymes. Physical Chemistry Chemical Physics. 18:20028-20032.   10.1039/c6cp00793g   AbstractWebsite

The significance of experiments that claim to simulate the properties of prebiotic small peptides and polypeptides as models of the polymers that may have preceded proteins is critically addressed. As discussed here, most of these experiments are based only on a small number of a larger set of amino acids that may have been present in the prebiotic environment, supported by both experimental simulations and the repertoire of organic compounds reported in carbonaceous chondrites. Model experiments with small peptides may offer some insights into the processes that contributed to generate the chemical environment leading to the emergence of informational oligomers, but not to the origin of proteins. The large body of circumstantial evidence indicating that catalytic RNA played a key role in the origin of protein synthesis during the early stages of cellular evolution implies that the emergence of the genetic code and of protein biosynthesis are no longer synonymous with the origin of life. Hence, reports on the abiotic synthesis of small catalytic peptides under potential prebiotic conditions do not provide information on the origin of triplet encoded protein biosynthesis, but in some cases may serve as models to understand the properties of the earliest proteins.

2013
Bennett, RV, Cleaves HJ, Davis JM, Sokolov DA, Orlando TM, Bada JL, Fernandez FM.  2013.  Desorption Electrospray Ionization Imaging Mass Spectrometry as a Tool for Investigating Model Prebiotic Reactions on Mineral Surfaces. Analytical Chemistry. 85:1276-1279.   10.1021/ac303202n   AbstractWebsite

Mineral-assisted thermal decomposition of formamide (HCONH2) is a heavily studied model prebiotic reaction that has offered valuable insights into the plausible pathways leading to the chemical building blocks of primordial informational polymers. To date, most efforts have focused on the analysis of formamide reaction products released in solution, although several studies have examined the role of mineral catalysts in promoting this chemistry. We show here that the direct investigation of reactive mineral surfaces by desorption electrospray ionization-mass spectrometry imaging (DESI-MSI) gives a new perspective on the important role of the mineral surface in the formation of reaction products. As a proof-of-principle example, we show that DESI-MSI allows interrogation of the molecular products produced on heterogeneous granite samples with minimal sample preparation. Purine and pyrimidine nucleobases and their derivatives are successfully detected by DESI-MSI, with a strong correlation of the spatial product distribution with the mineral microenvironment. To our knowledge, this study is the first application of DESI-MSI to the study of complex and porous mineral surfaces and their roles in chemical evolution. This DESI-MSI approach is generally applicable to a wide range of reactions or other processes involving minerals.

2011
Parker, ET, Cleaves HJ, Callahan MP, Dworkin JP, Glavin DP, Lazcano A, Bada JL.  2011.  Prebiotic Synthesis of Methionine and Other Sulfur-Containing Organic Compounds on the Primitive Earth: A Contemporary Reassessment Based on an Unpublished 1958 Stanley Miller Experiment. Origins of Life and Evolution of Biospheres. 41:201-212.   10.1007/s11084-010-9228-8   AbstractWebsite

Original extracts from an unpublished 1958 experiment conducted by the late Stanley L. Miller were recently found and analyzed using modern state-of-the-art analytical methods. The extracts were produced by the action of an electric discharge on a mixture of methane (CH(4)), hydrogen sulfide (H(2)S), ammonia (NH(3)), and carbon dioxide (CO(2)). Racemic methionine was formed in significant yields, together with other sulfur-bearing organic compounds. The formation of methionine and other compounds from a model prebiotic atmosphere that contained H(2)S suggests that this type of synthesis is robust under reducing conditions, which may have existed either in the global primitive atmosphere or in localized volcanic environments on the early Earth. The presence of a wide array of sulfur-containing organic compounds produced by the decomposition of methionine and cysteine indicates that in addition to abiotic synthetic processes, degradation of organic compounds on the primordial Earth could have been important in diversifying the inventory of molecules of biochemical significance not readily formed from other abiotic reactions, or derived from extraterrestrial delivery.

Kua, J, Bada JL.  2011.  Primordial Ocean Chemistry and its Compatibility with the RNA World. Origins of Life and Evolution of Biospheres. 41:553-558.   10.1007/s11084-011-9250-5   AbstractWebsite

We examine the stability of three key components needed to establish an RNA World under a range of potential conditions present on the early earth. The stability of ribose, cytosine, and the phosphodiester bond are estimated at different pH values and temperatures by extrapolating available experimental data. The conditions we have chosen range from highly acidic or alkaline hydrothermal vents, to the milder conditions in a primordial ocean at a range of atmospheric CO2 partial pressures.

Parker, ET, Cleaves HJ, Dworkin JP, Glavin DP, Callahan M, Aubrey A, Lazcano A, Bada JL.  2011.  Primordial synthesis of amines and amino acids in a 1958 Miller H2S-rich spark discharge experiment. Proceedings of the National Academy of Sciences of the United States of America. 108:5526-5531.   10.1073/pnas.1019191108   AbstractWebsite

Archived samples from a previously unreported 1958 Stanley Miller electric discharge experiment containing hydrogen sulfide (H2S) were recently discovered and analyzed using high-performance liquid chromatography and time-of-flight mass spectrometry. We report here the detection and quantification of primary amine-containing compounds in the original sample residues, which were produced via spark discharge using a gaseous mixture of H2S, CH4, NH3, and CO2. A total of 23 amino acids and 4 amines, including 7 organosulfur compounds, were detected in these samples. The major amino acids with chiral centers are racemic within the accuracy of the measurements, indicating that they are not contaminants introduced during sample storage. This experiment marks the first synthesis of sulfur amino acids from spark discharge experiments designed to imitate primordial environments. The relative yield of some amino acids, in particular the isomers of aminobutyric acid, are the highest ever found in a spark discharge experiment. The simulated primordial conditions used by Miller may serve as a model for early volcanic plume chemistry and provide insight to the possible roles such plumes may have played in abiotic organic synthesis. Additionally, the overall abundances of the synthesized amino acids in the presence of H2S are very similar to the abundances found in some carbonaceous meteorites, suggesting that H2S may have played an important role in prebiotic reactions in early solar system environments.

2009
Aubrey, AD, Cleaves HJ, Bada JL.  2009.  The Role of Submarine Hydrothermal Systems in the Synthesis of Amino Acids. Origins of Life and Evolution of Biospheres. 39:91-108.   10.1007/s11084-008-9153-2   AbstractWebsite

There is little consensus regarding the plausibility of organic synthesis in submarine hydrothermal systems (SHSs) and its possible relevance to the origin of life. The primary reason for the persistence of this debate is that most experimental high temperature and high-pressure organic synthesis studies have neglected important geochemical constraints with respect to source material composition. We report here the results of experiments exploring the potential for amino acid synthesis at high temperature from synthetic seawater solutions of varying composition. The synthesis of amino acids was examined as a function of temperature, heating time, starting material composition and concentration. Using very favorable reactant conditions (high concentrations of reactive, reduced species), small amounts of a limited set of amino acids are generated at moderate temperature conditions (similar to 125-175A degrees C) over short heating times of a few days, but even these products are significantly decomposed after exposure times of approximately 1 week. The high concentration dependence observed for these synthetic reactions are demonstrated by the fact that a 10-fold drop in concentration results in orders of magnitude lower yields of amino acids. There may be other synthetic mechanisms not studied herein that merit investigation, but the results are likely to be similar. We conclude that although amino acids can be generated from simple likely environmentally available precursors under SHS conditions, the equilibrium at high temperatures characteristic of SHSs favors net amino acid degradation rather than synthesis, and that synthesis at lower temperatures may be more favorable.

2004
Bada, JL.  2004.  How life began on Earth: a status report. Earth and Planetary Science Letters. 226:1-15.   10.1016/j.epsl.2004.07.036   AbstractWebsite

There are two fundamental requirements for life as we know it, liquid water and organic polymers, such as nucleic acids and proteins. Water provides the medium for chemical reactions and the polymers carry out the central biological functions of replication and catalysis. During the accretionary phase of the Earth, high surface temperatures would have made the presence of liquid water and an extensive organic carbon reservoir unlikely. As the Earth's surface cooled, water and simple organic compounds, derived from a variety of sources, would have begun to accumulate. This set the stage for the process of chemical evolution to begin in which one of the central facets was the synthesis of biologically important polymers, some of which had a variety of simple catalytic functions. Increasingly complex macromolecules were produced and eventually molecules with the ability to catalyze their own imperfect replication appeared. Thus began the processes of multiplication, heredity and variation, and this marked the point of both the origin of life and evolution. Once simple self-replicating entities originated, they evolved first into the RNA World and eventually to the DNA/Protein World, which had all the attributes of modern biology. If the basic components water and organic polymers were, or are, present on other bodies in our solar system and beyond, it is reasonable to assume that a similar series of steps that gave rise of life on Earth could occur elsewhere. (C) 2004 Elsevier B.V. All rights reserved.

1995
McDonald, GD, Bada JL.  1995.  A Search for Endogenous Amino-Acids in the Martian Meteorite Eeta79001. Geochimica Et Cosmochimica Acta. 59:1179-1184.   10.1016/0016-7037(95)00033-v   AbstractWebsite

The Antarctic shergottite EETA 79001 is believed to be an impact-ejected fragment of the planet Mars. Samples of the carbonate (white druse) and the basaltic (lithology A) components from this meteorite have been found to contain amino acids at a level of approximately 1 ppm and 0.4 ppm, respectively. The detected amino acids consist almost exclusively of the L-enantiomers of the amino acids commonly found in proteins, and are thus terrestrial contaminants. There is no indication of the presence of alpha-aminoisobutyric acid, one of the most abundant amino acids in several carbonaceous chondrites. The relative abundances of amino acids in the druse material resemble those in Antarctic ice, suggesting that the source of the amino acids may be ice meltwater. The level of amino acids in EETA79001 druse is not by itself sufficient to account for the 600-700 ppm of volatile C reported in druse samples and suggested to be from endogenous martian organic material. However, estimates of total terrestrial organic C present in the druse material based on our amino acid analyses and the organic C content of polar ice can account for most of the reported putative organic C in EETA 79001 druse.

Bada, JL, Miller SL, Zhao MX.  1995.  The Stability of Amino-Acids at Submarine Hydrothermal Vent Temperatures. Origins of Life and Evolution of the Biosphere. 25:111-118.   10.1007/bf01581577   AbstractWebsite

It has been postulated that amino acid stability at hydrothermal vent temperatures is controlled by a metastable thermodynamic equilibrium rather than by kinetics. Experiments reported here demonstrate that the amino acids are irreversibly destroyed by heating at 240 degrees C and that quasi-equilibrium calculations give misleading descriptions of the experimental observations. Equilibrium thermodynamic calculations are not applicable to organic compounds under high-temperature submarine vent conditions.