Prebiotic Chemistry

What do you know about evolutionary theory? Or, maybe there are two questions here: (1) What do you think you know; (2) What do you actually know?

Quite irrespective of whether individuals believe in evolution or they are opposed to it, most people probably would have to acknowledge that they know almost nothing at all about the actual nuts and bolts of the technical issues at the heart of evolutionary theory. Their beliefs concerning this matter -- whatever the character of those beliefs might be -- is, for the most part, likely to be framed by, and filtered through, two themes: (a) a largely unexamined acceptance of the opinion of others; (b) the extent to which evolutionary theory makes carrying on with the rest of their philosophical or religious perspective either easier or more difficult to continue to do.

Seeking the truth should neither be a function of blindly following the beliefs of other individuals, nor should that process be a function of what one finds easy or difficult to do, Therefore, irrespective of what your conceptual orientation concerning evolution might be, this book was written to challenge readers to critically reflect on various problems so that individuals might be able to work their way toward gaining greater insight into a variety of issues that swirl about the topic of evolution.
Finally, Evolution Unredacted offers a critical analysis of several landmark legal decisions involving the dispute between proponents of evolution and advocates for creationism -- namely, McLean v. Arkansas Board of Education and Kitzmiller, et al v. Dover Area School District, et al. More specifically, the final chapter of Evolution Unredacted engages the evolution v. creationism debate through the filters of the Establishment Clause of the First Amendment and Article IV, Section 4 of the Constitution.

The results of the foregoing analysis are likely to surprise the reader. Moreover, those results tend to entail a variety of implications for the process of education.

The present paper offers a review of recent (post-1980) work on amino acid adsorption and thermal reactivity on oxide and sulfide minerals. This review is performed in the general frame of evaluating Bernal's hypothesis of prebiotic polymerization in the adsorbed state, but written from a surface scientist's point of view. After a general discussion of the thermodynamics of the problem and exactly what effects surfaces should have to make adsorbed-state polymerization a viable scenario, we examine some practical difficulties in experimental design and their bearing on the conclusions that can be drawn from extant works, including the relevance of the various available characterization techniques. We then present the state of the art concerning the mechanisms of the interactions of amino acids with mineral surfaces, including results from prebiotic chemistry-oriented studies, but also from several different fields of application, and discuss the likely consequences for adsorption selectivities. Finally, we briefly summarize the data concerning thermally activated amide bond formation of adsorbed amino acids without activating agents. The reality of the phenomenon is established beyond any doubt, but our understanding of its mechanism and therefore of its prebiotic potential is very fragmentary. The review concludes with a discussion of future work needed to fill the most conspicuous gaps in our knowledge of amino acids/mineral surfaces systems and their reactivity.

The current book is not about trying to prove the truth of this or that scientific or religious account about the origins of either human beings, in particular, or life, in general. ‘The Origin of Life' is about the problems surrounding the process of interpreting empirical evidence and subjecting that data to various methods of rigorous critical reflection.

Context: Fructooligosaccharides (FOS) are known as oligofructanes, oligosaccharides or oligofructose, which fall within the concept of prebiotics. One of the methods most commonly used in the industry for quantification and quality control nutraceutical substances classification is the method of high performance liquid chromatography (HPLC).

Aims: To develop a procedure for the determination of FOS by HPLC in raw materials and a prebiotic ice cream.

Methods: For the chromatographic separation, an HPLC was used with a refractive index detector (IR). The separation was performed using two columns coupled Sugar-pak I™ using an isocratic procedure with water type 1 at 0.35 mL/min. Kestose (GF2), nistose (GF3) and fructofuranosylnystose (GF4) were used as standards. Robustness was assessed by applying the Youden and Steiner test.

Results: Good linear correlations were obtained (y = 14191.4470 x + 285684.2, r2 = 0.9904) within the concentration range of 8.0-12.0 mg/mL. The FOS recoveries were 99.5% with the intra-day and inter-day relative standard deviation (RSD) less than 0.8%. The robustness test showed that the temperature parameters of the column and flow velocity are critical factors in the method.

Conclusions: This reliable, simple and cost-effective method could be applied to the routine monitoring of FOS (GF2, GF3, and GF4) in raw materials and prebiotic ice creams.

It is widely agreed that the standard genetic code must have been preceded by a simpler code that encoded fewer amino acids. How this simpler code could have expanded into the standard genetic code is not well understood because most changes to the code are costly. Taking inspiration from the recently synthesized six-letter code, we propose a novel hypothesis: the initial genetic code consisted of only two letters, G and C, and then expanded the number of available codons via the introduction of an additional pair of letters, A and U. Various lines of evidence, including the relative prebiotic abundance of the earliest assigned amino acids, the balance of their hydrophobicity, and the higher GC content in genome coding regions, indicate that the original two nucleotides were indeed G and C. This process of code expansion probably started with the third base, continued with the second base, and ended up as the standard genetic code when the second pair of letters was introduced into the first base. The proposed process is consistent with the available empirical evidence, and it uniquely avoids the problem of costly code changes by positing instead that the code expanded its capacity via the creation of new codons with extra letters.

There are growing indications that life began in a radioactive beach environment. A geologic framework for the origin or support of life in a Hadean heavy mineral placer beach has been developed, based on the unique chemical properties of the lower-electronic actinides, which act as nuclear fissile and fertile fuels, radiolytic energy sources, oligomer catalysts, and coordinating ions (along with mineralogically associated lanthanides) for prototypical prebiotic homonuclear and dinuclear metalloenzymes. A four-factor nuclear reactor model was constructed to estimate how much uranium would have been required to initiate a sustainable fission reaction within a placer beach sand 4.3 billion years ago. It was calculated that about 1-8 weight percent of the sand would have to have been uraninite, depending on the weight percent, uranium enrichment, and quantity of neutron poisons present within the remaining placer minerals.

This study aims to investigate the effect of fructooligosaccharide (FOS) (0.5, 1, 2, 3, and 4%) supplementation on the growth and survival of Bifidobacterium breve and Bifidobacterium longum in glucose, fructose, lactose, and sucrose (2, 3, and 4%) systems with 24-h growth and 10-day survival assays at 37°C. FOS supplementation showed a higher growth-promoting effect on B. longum than B. breve in various sugar systems. The highest percentage of increase in growth index, 78.5%, was observed with 4% sucrose supplemented with 0.5% FOS in B. longum. In comparison, the highest percentage increase in growth index, 5.6 and 6.6%, was observed in the presence of 2% glucose and 4% lactose supplemented with 0.5% FOS in B. breve. In survival assay, FOS supplementation (0.5-4%) in a 2% lactose system showed the highest positive effect on the cell viability of B. longum on day-10. As for B. breve, FOS supplementation (1 and 2%) in the 2% sucrose system showed the highest positive effect on the cell viability, followed by FOS supplementation (0.5, 3, and 4%) in 2% sucrose and FOS supplementation (3 and 4%) in 2% lactose on day-10. This study demonstrated that the efficacy of FOS supplementation was depended on its concentration, sugar system and its concentration, and Bifidobacterium strain.

The Strecker reaction of aldehydes with ammonia and hydrogen cyanide first leads to α-aminonitriles, which are then hydrolyzed to α-amino acids. However, before reacting with water, these aminonitriles can be trapped by aminothiols, such as cysteine or homocysteine, to give 5- or 6-membered ring heterocycles, which in turn are hydrolyzed to dipeptides. We propose that this two-step process enabled the formation of thiol-containing dipeptides in the primitive ocean. These small peptides are able to promote the formation of other peptide bonds and of heterocyclic molecules. Theoretical calculations support our experimental results. They predict that α-aminonitriles should be more reactive than other nitriles, and that imidazoles should be formed from transiently formed amidinonitriles. Overall, this set of reactions delineates a possible early stage of the development of organic chemistry, hence of life, on Earth dominated by nitriles and thiol-rich peptides (TRP).

The existence of the ribose moiety in biomolecules poses two problems for prebiotic chemistry. First, the exclusive presence of the furanose isomer in RNA has to be accounted for since furanose is a minor form in solution and does not exist in crystals. Second, all D-ribose polymorphs are unstable in aqueous medium so that a stabilization mechanism has to be invoked. We observed that the adsorption on mineral surfaces as amorphous silica protects the sugar from degradation processes. Moreover, this silica surface, used as realistic chert model, is able to increase significantly the proportion of ribofuranose compared to ribopyranose forms. The interaction between surface and sugar was analyzed by 13C NMR. Our results show a very significant chemical and thermal stabilization of the adsorbed sugar by a silica surface and an almost twofold increase of ribofuranose compared to ribose in solution.

This study aimed to investigate the effect of mannan-oligosaccharide (MOS) on the lipogram and selected organ functions in hyperlipidemic rats. Animals were subjected to different treatments for 60 days. Balanced basal diet was supplied to control rats; saturated high fat- and/or MOS-contained diets were supplied to tested rats. Sera were collected on escalating times and total lipids, cholesterol, triacylglycerols, HDL-C, LDL-C, VLDL-C, AST, ALT, urea and creatinine were evaluated. On the last day, rats were sacrificed and the kidneys, liver, heart with aorta were picked out for histopathology. The results of MOS-treated group revealed significant decrease in total lipids, cholesterol, LDL-C, VLDL-C, AST, ALT, urea and creatinine with significant increase in HDL-C. Histopathological findings in the tested organs have been ameliorated with MOS, comparing with those in hyperlipidemic rats. The obtained data may give MOS the potential of antihyperlipidemic activity for prophylaxis and treatment of hyperlipidemia and related diseases.

The synthesis and crystal structure of rhodamine 590 acid phthalate (RhAP) have been reported. This novel solid-state rhodamine derivative not only has a longer fluorescence lifetime compared to rhodamine solid-state matrixes where emission is quenched but also possesses strong nonlinear optical characteristics. The static and dynamic firstand second-order hyperpolarizabilities were calculated using the time-dependent density functional theory at the B3LYP/6-31+G* level. The computed static values of β and γ of RhAP by the X-ray diffraction (XRD) structure were 31.9 × 10 −30 and 199.0 × 10 −36 esu, respectively. These values were about 62 times larger than the corresponding values in urea, an already well-known nonlinear optical material. The second-order hyperpolarizability of the compound was determined experimentally by measuring the two-photon absorption cross section using intensity-modulated light fields. The reported compound, excitable at near-infrared, exhibited frequency upconversion with the two-photon absorption coefficient enhanced by two orders of magnitude compared to that of the dye solution. Hosting the dye in the solid, at high concentrations, exploits the nonlinearity of the dye itself as well as results in significant excitonic effects including formation of broad exciton band and superradiance.

We show that carbonaceous chondrite meteorites actively and selectively catalyze the formation of relevant prebiotic molecules from formamide in aqueous media. Specific catalytic behaviours are observed, depending on the origin and composition of the chondrites and on the type of water present in the system (activity: thermal > seawater > pure). We report the one-pot synthesis of all the natural nucleobases, of aminoacids and of eight carboxylic acids (forming, from pyruvic acid to citric acid, a continuous series encompassing a large part of the extant Krebs cycle). These data shape a general prebiotic scenario consisting of carbonaceous meteorites acting as catalysts and of a volcanic-like environment providing heat, thermal waters and formamide. This scenario also applies to the other solar system locations that experienced rich delivery of carbonaceous materials, and whose physical-chemical conditions could have allowed chemical evolution. It is assumed that meteorites played a role in the origin of life, behaving as carriers of organic compounds during the Heavy Bombardment period on Earth 1,2 , before the earliest appearance of living organisms 3. Carbonaceous chondrites are ancient space objects containing minerals condensed in the Solar Nebula or inherited from the delivery from nearby stars, partially modified by secondary processing histories 4. They derive from asteroids that did not undergo planetary differentiation 5 or from outer regions of the protoplanetary disk, and are characterized by reactive minerals, high water content and organic molecules, as amino acids, in the range of parts-per-billion (ppb) 6,7. Theoretical and experimental models suggest that a part of the organic materials present in carbonaceous chondrites could have been synthesized before the parent body accretion and then evolve under hydrothermal alteration after accretion inside the parent body 8 at temperature ranging from 100 °C to 150 °C due to radioactive phenomena 9,10. It has been envisioned that water alteration in carbonaceous asteroids occurred under quite static conditions because they were " cooked " slowly and with restricted water availability (e.g. from bounded water in phyllosilicates, hydroxides or other minerals) 11. Current evidence suggests a significant and heterogeneous water content in the parent bodies of carbonaceous chondrites (0–25 wt. % H 2 O) 8. Carbonaceous chondrites exhibit signs of static aqueous alteration that generated characteristic minerals in the fine-grained matrix, where reactions could take place as a function of the increasing complexity 12. Catalytic properties of meteorites in prebiotic chemistry were observed related to thermal processes of neat formamide (NH 2 CHO) 13,14. Meteorites perform as catalysts better than terrestrial minerals, as exemplified by the one-pot formation of ribo-and 2'-deoxyribo nucleosides upon irradiation of NH 2 CHO with high-energy proton beams, mimicking the effect of solar wind 15. Comments on the prebiotic relevance of NH 2 CHO are in Supplementary text SI # 1. Results on the use of HCN in presence of copper and UV light and involving a meteorite in the synthesis of some prebiotically relevant specific intermediates have been reported 16. The role of water in prebiotic chemistry is controversial, due to its nucleophile character inducing solvoly-sis reactions. NH 2 CHO and HCN are degraded in water, which might have limited their efficacy as prebiotic

Geologic settings capable of driving prebiotic oligomer synthesis reactions remain a relatively unexplored aspect of origins of life research. Natural nuclear reactors are an example of Precambrian energy sources that produced unique temperature fluctuations. Heat transfer models indicate that water-moderated, convectively-cooled natural fission reactors in porous host rocks create temperature oscillations that resemble those employed in polymerase chain reaction (PCR) devices to artificially amplify oligonucleotides. This temperature profile is characterized by short-duration pulses up to 70-100°C, followed by a sustained period of temperatures in the range of 30-70°C, and finally a period of relaxation to ambient temperatures until the cycle is restarted by a fresh influx of pore water.  For a given reactor configuration, temperature maxima and the time required to relax to ambient temperatures depend most strongly on the aggregate effect of host rock permeability in decreasing the thermal expansion and increasing the viscosity and evaporation temperature of the pore fluids.  Once formed, fission-fueled reactors can sustain multi-kilowatt-level power production for 105-106 years, ensuring microenvironmental longevity and chemical output. The model outputs indicate that organic synthesis on young planetary bodies with a sizeable reservoir of fissile material can involve more sophisticated energy dissipation pathways than modern terrestrial analog settings alone would suggest.

Amphiphilic bilayer membrane structures (vesicles) have been postulated to have been abiotically formed and spontaneously assemble on the prebiotic Earth, providing compartmentalization for the origin of life. These vesicles are similar to modern cellular membranes and can serve to contain water-soluble species, concentrate species, and have the potential to catalyze reactions. The origin of the use of photochemical energy in metabolism (i.e. energy transduction) is one of the central issues in the origin of life. This includes such questions as how energy transduction may have occurred before complex enzymatic systems, such as required by contemporary photosynthesis, had developed and how simple a photochemical system is possible. It has been postulated that vesicle structures developed the ability to capture and transduce light, providing energy for reactions. It has also been shown that pH gradients across the membrane surface can be photochemically created, but coupling these to drive chemical reactions has been difficult. Colloidal semiconducting mineral particles are known to photochemically drive redox chemistry. We propose that encapsulation of these particles has the potential to provide a source of energy transduction inside vesicles, and thereby drive protocellular chemistry, and represents a model system for early photosynthesis. In our experiments we show that TiO2 particles, in the ~20 nm size range, can be incorporated into vesicles and retain their photoactivity through the dehydration/rehydration cycles that have been shown to concentrate species inside a vesicle.

Uno de los mayores retos de las investigaciones espaciales es la búsqueda de señales de vida pasada o presente en nuestro Sistema Solar, y evidencia de ella son las moléculas o compuestos orgánicos. Más allá de su búsqueda, los mayores problemas son determinar si su origen es biótico-producto de un organismo-o abiótico-producto de procesos químicos-, y sobre todo, para que sean evidencia de vida extraterrestre es necesario que se encuentre variedad de estas moléculas y en considerables concentraciones (1). Precursores de estas moléculas son los átomos de Carbono, tan versátil como universal; y monómeros de aminoácidos, lípidos, nucleobases y azúcares han sido encontrados en meteoritos carbonosos, en los que, luego de su síntesis, viajan por el espacio hasta la Tierra y otros cuerpos (2). Es así que, están expuestas durante su travesía a condiciones espaciales hostiles que juegan un rol importante en la evolución química de la materia orgánica, como la radiación; pero se ha demostrado que el polvo de meteoritos les confiere resistencia, como muestran los resultados del experimento AMINO en la ISS: los aminoácidos en polvo de meteorito resisten las condiciones espaciales y la radiación UV mucho más que los que se evaluaron en forma libre (3). Si la vida usa aminoácidos y azúcares para las estructuras de las proteínas y ácidos nucleicos, y dada la abundancia de estos componentes en el espacio, se puede sugerir que la vida está evolucionando en algún cuerpo de nuestro Sistema Solar, pero el hecho de que no exista aún evidencia de ello nos acerca a conceptos de importancia astrobiológica, como " límites de vida " y " habitabilidad planetaria " y conduce a otros autores a sugerir que el desarrollo de la vida sigue un patrón universal en todos los niveles. Aún con muchas preguntas pendientes de respuestas, es un hecho que entender los parámetros físicos y químicos de la vida nos permitirá no sólo descubrir señales de vida en otros planetas, sino también entender nuestro ambiente terrestre (2,4,5). Palabras claves: moléculas orgánicas, aminoácidos, radiación UV, habitabilidad planetaria. Abstract One of the biggest challenges of space research is the search for signs of past or present life in our Solar System, and evidence of it are organic compounds. Beyond search, the biggest problems are to determine whether its origin is biotic-product of an organism-or abiotic-product of chemical processes-, and above all, to be evidence of extraterrestrial life need to be variety of these molecules and considerable concentrations (1). Precursors of these molecules are carbon atoms, as versatile as universal; monomers and amino acids, lipids, sugars and nucleobases have been found in carbonaceous meteorites, which after its synthesis, travel through space to Earth and other bodies (2). Thus, during their journey are exposed to hostile space conditions, wich play an important role in the chemical evolution of organic matter, such as radiation. But it has shown that dust meteor confers resistance, as the results of the experiment AMINO the ISS: amino acid powder meteorite resist spatial conditions and UV radiation much more than those evaluated in free form (3). If life uses amino acids and sugars for the structures of proteins and nucleic acids, and given the abundance of these components in space, can suggest that life is evolving in a surface in our solar system, but the fact