Publications

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2016
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.

2014
Parker, ET, Cleaves JH, Burton AS, Glavin DP, Dworkin JP, Zhou MS, Bada JL, Fernandez FM.  2014.  Conducting Miller-Urey experiments. Jove-Journal of Visualized Experiments.   10.3791/51039   AbstractWebsite

In 1953, Stanley Miller reported the production of biomolecules from simple gaseous starting materials, using an apparatus constructed to simulate the primordial Earth's atmosphere-ocean system. Miller introduced 200 ml of water, 100 mmHg of H-2, 200 mmHg of CH4, and 200 mmHg of NH3 into the apparatus, then subjected this mixture, under reflux, to an electric discharge for a week, while the water was simultaneously heated. The purpose of this manuscript is to provide the reader with a general experimental protocol that can be used to conduct a Miller-Urey type spark discharge experiment, using a simplified 3 L reaction flask. Since the experiment involves exposing inflammable gases to a high voltage electric discharge, it is worth highlighting important steps that reduce the risk of explosion. The general procedures described in this work can be extrapolated to design and conduct a wide variety of electric discharge experiments simulating primitive planetary environments.

2011
Grew, ES, Bada JL, Hazen RM.  2011.  Borate Minerals and Origin of the RNA World. Origins of Life and Evolution of Biospheres. 41:307-316.   10.1007/s11084-010-9233-y   AbstractWebsite

The RNA World is generally thought to have been an important link between purely prebiotic (>3.7 Ga) chemistry and modern DNA/protein biochemistry. One concern about the RNA World hypothesis is the geochemical stability of ribose, the sugar moiety of RNA. Prebiotic stabilization of ribose by solutions associated with borate minerals, notably colemanite, ulexite, and kernite, has been proposed as one resolution to this difficulty. However, a critical unresolved issue is whether borate minerals existed in sufficient quantities on the primitive Earth, especially in the period when prebiotic synthesis processes leading to RNA took place. Although the oldest reported colemanite and ulexite are 330 Ma, and the oldest reported kernite, 19 Ma, boron isotope data and geologic context are consistent with an evaporitic borate precursor to 2400-2100 Ma borate deposits in the Liaoning and Jilin Provinces, China, as well as to tourmaline-group minerals at 33003450 Ma in the Barberton belt, South Africa. The oldest boron minerals for which the age of crystallization could be determined are the metamorphic tourmaline species schorl and dravite in the Isua complex (metamorphism between ca. 3650 and ca. 3600 Ma). Whether borates such as colemanite, ulexite and kernite were present in the Hadean (>4000 Ma) at the critical juncture when prebiotic molecules such as ribose required stabilization depends on whether a granitic continental crust had yet differentiated, because in its absence we see no means for boron to be sufficiently concentrated for borates to be precipitated.

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
Cleaves, HJ, Aubrey AD, Bada JL.  2009.  An Evaluation of the Critical Parameters for Abiotic Peptide Synthesis in Submarine Hydrothermal Systems. Origins of Life and Evolution of Biospheres. 39:109-126.   10.1007/s11084-008-9154-1   AbstractWebsite

It has been proposed that oligopeptides may be formed in submarine hydrothermal systems (SHSs). Oligopeptides have been synthesized previously under simulated SHS conditions which are likely geochemically implausible. We have herein investigated the oligomerization of glycine under SHS-like conditions with respect to the limitations imposed by starting amino acid concentration, heating time, and temperature. When 10(-1) M glycine solutions were heated at 250A degrees C for < 20 min glycine oligomers up to tetramers and diketopiperazine (DKP) were detectable. At 200A degrees C, less oligomerization was noted. Peptides beyond glycylglycine (gly(2)) and DKP were not detected below 150A degrees C. At 10(-2) M initial glycine concentration and below, only gly(2), DKP, and gly(3) were detected, and then only above 200A degrees C at < 20 min reaction time. Gly(3) was undetectable at longer reaction times. The major parameters limiting peptide synthesis in SHSs appear to be concentration, time, and temperature. Given the expected low concentrations of amino acids, the long residence times and range of temperatures in SHSs, it is unlikely that SHS environments were robust sources of even simple peptides. Possible unexplored solutions to the problems presented here are also discussed.

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.

2003
Kminek, G, Bada JL, Pogliano K, Ward JF.  2003.  Radiation-dependent limit for the viability of bacterial spores in halite fluid inclusions and on Mars. Radiation Research. 159:722-729.   10.1667/0033-7587(2003)159[0722:rlftvo]2.0.co;2   AbstractWebsite

When claims for the long-term survival of viable organisms are made, either within terrestrial minerals or on Mars, considerations should be made of the limitations imposed by the naturally occurring radiation dose to which they have been exposed. We investigated the effect of ionizing radiation on different bacterial spores by measuring the inactivation constants for B. subtilis and S. marismortui spores in solution as well as for dry spores of B. subtilis and B. thuringiensis. S. marismortui is a halophilic spore that is genetically similar to the recently discovered 2-9-3 bacterium from a halite fluid inclusion, claimed to be 250 million years old (Vreeland et al, Nature 407, 897-900, 2000). B. thuringiensis is a soil bacterium that is genetically similar to the human pathogens B. anthracis and B. cereus (Helgason et al., Appl. Environ. Microbiol 66, 2627-2630, 2000). To relate the inactivation constant to some realistic environments, we calculated the radiation regimen in a halite fluid inclusion and in the Martian subsurface over time. Our conclusion is that the ionizing dose of radiation in those environments limits the survival of viable bacterial spores over long periods. In the absence of an active repair mechanism in the dormant state, the long-term survival of spores is limited to less than 109 million years in halite fluid inclusions, to 100 to 160 million years in the Martian subsurface below 3 m, and to less than 600,000 years in the uppermost meter of Mars. (C) 2003 by Radiation Research Society.

1994
Becker, L, Bada JL, Winans RE, Bunch TE.  1994.  Fullerenes in Allende Meteorite. Nature. 372:507-507.   10.1038/372507a0   Website