Converting raw energy into biological energy

...the answer is just chemistry.

Certainly there is an article on the subject you could post a link to...

Doddy writes:You do have a point Rob - the conditions that chemists can create are likely to be far more favourable to the creation of life than was present primordially. I once read that it was like a golfer putting a golfball into the hole, then surmising that wind, rain, tornadoes and earthquakes could have done the same, given enough time.However, it isn't especially likely that life originated in this manner. Not only are these steps quite probably not the ones that occurred, but a ribozyme might not even be the first sort of life (if the RNA world isn't true).But then, a few humans have only looked at this problem for a few dozen years, whereas there were billions of years and billions of planets for this to occur randomly. I don't care how smart you think humans are, or how dumb you think chemical reactions are - I have no problem believing that this would have happened.

Rob writes:The smallest self replicating system that is emperical already exists.

And even though ATP appears to be relatively simple, the way it is made isn't simple; a multitude of functions are involved.

Talk about assuming the existence of the very thing your trying to explain.

You mean taking already formed biological machines and helping the process along with advanced technology and intelligent doctors?

No... It is my position that ATP cannot be made in nature without ATP synthase.

And the same postulated conditions produced all of these results? Or did it take huge differences in environment to produce different stages?

Here, novel experimental results are reported that ATP are synthesized from adenosine-5-diphosphate (ADP) and ADP from adenosine-5-monophosphate (AMP) by spontaneous phosphorylation in aqueous solution containing calcium phosphate and cyanate. The phosphorylation reactions proceeded only when cyanate was used as a condensing reagent. This recyclable molecule is observed in cosmic clouds, suggesting it was present in prebiotic times.The reaction is strongly dependent on the pH, and a pH of 5.5-6.0 is the most effective. We must ask, is this pH range likely to have existed in primitive Earth conditions. Miller and Orgel (1974) have suggested that pH of the primitive ocean was weakly basic between 8.0-8.5 similar to that of the present ocean. However, the early primitive Earth would have been covered with an atmosphere of relatively high partial pressure of carbon dioxide (Rubey, 1955; Abelson, 1966; Kasting and Ackerman, 1987). In that case, the sea water would have been weakly acidic. This was actually checked in a laboratory experiment. A fresh sea water (from Sea of Japan at the sea shore of Kanazawa) showed a pH of 8.26. When carbon dioxide was poured over the sea water in the Erlenmeyer flask (not bubbling), the pH stayed at a value of 4.95 after decreasing gradually. Then, calcium carbonate (1.0% of the sea water) was added in the flask still pouring carbon dioxide. In this case, the pH increased to a value of 6.03.It was reported that AMP was constantly synthesized by the phosphorylation of adenosine in a long-term discharge experiment, which simulated the recycling system of the water and the other volatile substances on the primitive Earth surface (Yamagata et al., 1979, 1981). The condensation was demonstrated to be due to the formation of cyanate (Yamagata and Mohri, 1982). Cyanate is a condensing reagent that can be hydrolyzed to the gaseous components, carbon dioxide and ammonia. The recyclability would be a necessary condition imposed on prebiotic condensing reagents, because the prebiotic evolution had to continue through the geologic time. Cyanic acid or isocyanic acid would be a true prebiotic condensing reagent, since the latter molecule that is the tautomer of cyanic acid has been observed in the interstellar clouds (Rank et al., 1971).In conclusion, the present phosporylation reactions are summarized as follows:
NMP + Pi + Ca2+ + cyanate ’ NDP
NDP + Pi + Ca2+ + cyanate ’ NTP
NMP + hydroxyapatite[or Ca3 (PO4 )2 or CaHPO4 ·2H2 O] + cyanate ’ NDP
NDP + hydroxyapatite[or Ca3 (PO4 )2 or CaHPO4 ·2H2 O] + cyanate ’ NTPRecently, it was found that water-soluble phosphate and polyphosphates were produced through the volcanic activity (Yamagata et al., 1991). Most of the phosphates from volcanoes eventually would have been converted into water-insoluble calcium phosphate by the reaction with calcium ion in the ocean. Rocks on the Earth as well as meteorites contain most phosphate in the form of apatite. In the weathering of the rocks the apatite would have been released into the ocean from the rocks. These conditions on the primitive Earth have been simulated in the present experiments. Probable low temperature and weakly acidic conditions of the primitive ocean would have made it possible to survive and to accumulate the essential prebiotic molecules. Miller and Parris (1964) reported the formation of pyrophosphate from hydroxyapatite and cyanate. The present reactions are closely related to their reaction.

Orgel writes:Molecules that stay together evolve together.

The RNA World model for prebiotic evolution posits the selection of catalytic/template RNAs from random populations ... This low probability (of random interactions) could be overcome if the molecules capable of productive recombination were redundant, with many nonhomologous but functionally equivalent RNAs being present in a random population ... Parallel SELEX experiments showed that at least one in 106 random 20-mers binds to the P5.1 stem-loop of Bacillus subtilis RNase P RNA with affinities equal to that of its naturally occurring partner. This high frequency predicts that a single RNA in an RNA World would encounter multiple interacting RNAs within its lifetime, supporting recombination as a plausible mechanism for prebiotic RNA evolution. The large number of equivalent species implies that the selection of any single interacting species in the RNA World would be a contingent event, i.e., one resulting from historical accident.

Orgel writes:The inevitable conclusion of this survey of nucleotide synthesis is that there is at present no convincing, prebiotic total synthesis of any of the nucleotides.

Prebiotic chemistry experiments search to explain the origins and properties of chemical structures and reactions which may have been involved in the life emergence (for recent reviews see Eschenmoser and Loewenthal, 1992; Sutherland and Whitfield, 1997; Maurel and Décout, 1999). Small molecules present in the primitive Earth atmosphere such as water, carbon monoxide, sulfur dioxide, methane, dinitrogen (but not dioxygen) could react to lead to the elementary building blocks, ammonia, hydrogen cyanide, formaldehyde, acetonitrile, acrylonitrile, cyanogen and cyanoacetylene. Cosmic rays, ionizing radiations, electric discharges and radioactive process induced ion-molecule and radical reactions which led to these building blocks. From these molecules, formation of amino acids ( Miller and Miller; Joshi and Pathak, 1975; Kobayashi et al., 1998) and nucleic acid bases ( Or and Or; Or and Kimball, 1961; Ferris and Orgel, 1966; Robertson and Miller, 1995; Miyakawa et al., 1999) such as adenine 1 (Fig. 1, C5H5N5: pentamer of hydrogen cyanide) under prebiotic conditions could be explained. Many prebiotic molecules could already have been present in comets such as adenine detected into comet Halley dust. Or suggested that comets might already have brought to the Earth biochemical precursors necessary for emergence of life (Or, 1961; Or et al., 1992). Delsemme emphasized more and more evidences support that an intense bombardment of comets has brought to the Earth all the carbon compounds present in organic molecules used by life ( Delsemme and Delsemme 2000).

In the search of chemical prebiotic routes which could lead from nucleic acid bases to building blocks capable of polymerizing to form nucleic acids strands, we are investigating reactions of adenine with different aldehydes under presumably prebiotic conditions. Such reactions could have led to nucleoside and nucleoside-like building blocks endowed with catalytic properties necessary for life. Previously, Fel'dman (1962) reported slow reactions of adenine with formaldehyde in aqueous solution at room temperature under neutral conditions to form adducts on the 6-amino group and/or the 9-nitrogen atom.Pyruvic acid being a central intermediate in the present metabolism, we studied reactivity of the corresponding aldehyde, pyruvic aldehyde 2 (methylglyoxal), with adenine 1 (Fig. 1) and we are reporting here these results. Pyruvaldehyde could have been produced under prebiotic conditions by retroaldolization from complex mixtures of sugars formed by the formose reaction. It was detected in caramel ( Tomasik et al., 1989) and alkaline decomposition of hexoses such as Image-mannose, Image-xylose and Image-glucose which affords pyruvaldehyde hydrate (Evans, 1942; Feather and Harris, 1973). Such decompositions of sugars could have been a source of various prebiotic molecules like aldehydes and heterocycles.

Careful examination of the present metabolism and in vitro selection of various catalytic RNAs strongly support the “RNA World” hypothesis of the origin of life. However, in this scenario, the difficult prebiotic synthesis of ribose and consequently of nucleotidesnext term remain a major problem. In order to overcome this problem and obtain nucleoside analogs, we are investigating reactions of the nucleic acid base, adenine 1, with different aldehydes under presumably prebiotic conditions. In the reaction of adenine and pyruvaldehyde 2 in water, we report here the formation in high yield of two isomeric products. These compounds possessing alcohols functions as nucleosides result from condensation of two molecules of pyruvaldehyde on the 6-amino group of one adenine molecule.

In prebiotic scenarios biopolymers can be thought of as condensation products of abiotically formed monomers. Polymers (polysaccharides, peptides, and polynucleotides) will not spontaneously form in an aqueous solution from their monomers because of the standard-state Gibbs free-energy change ... In the polymerization process of nucleic acids extant organisms activate the monomers by converting them to phosphorylated derivatives and then utilize the favorable free energy of phosphate hydrolysis to drive the reaction. Does this present day process mimic spontaneously occurring prebiotic reactions, thus representing a sort of biochemiomimesis descending from ancient pathways, or should it be considered a fully novel cellular invention? ... we report the efficient phosphorylation of nucleosides occurring in formamide on numerous phosphate minerals. Consequently, ... activated monomers can form in prebiotic conditions in a liquid, non-aqueous environment in the presence of phosphate minerals in conditions compatible with the thermodynamics of polymerization.

Recent studies have shown how interactions of the ”RNA world’ with lipids may have been mutually beneficial for both vesicle formation and RNA replication (Chen et al., 2004). In lipid vesicles, replicating RNA molecules profit by being segregated away from non-replicating ”free-loading’ RNAs that would otherwise benefit from efficient RNA polymerase action. Conversely, the ability of RNA molecules to replicate would have allowed vesicles to grow through increased osmotic pressure (Chen et al., 2004). In this scheme, the more successful vesicle/replicating RNA combinations would expand the fastest and would thus be more likely to split into daughter vesicles, thereby fulfilling many of the key requirements for the initiation of primordial life.Less progress has been made in showing how mutually beneficial interactions could have arisen between the RNA and early protein world. In vitro selection strategies have shown that RNA molecules are capable of carrying out several steps required for amino acid activation and peptide bond formation (Chapple et al., 2003; Ferreira and Coutinho, 1993; Huang et al., 2000; Johnston et al., 2001; Kumar and Yarus, 2001). However, it is unclear how the acquisition of these enzymic activities would have been subject to immediate selection in the primordial environment (Orgel, 1989).Here I propose a scheme that integrates nucleic acid and protein function in a way that allows the mutual co-evolution of nucleic acid-dependent protein synthesis and nucleic acid-dependent nucleic acid replication. The model proposes a very early association between nucleic acid and protein polymers in the primordial development of life. It suggests a specific role for amyloid; a protein aggregate in which main chain -sheet interactions stabilize the formation of fibres. Predictions from the model are consistent with recently published observations.This proposal differs from the prevailing ”RNA-world’ model of pre-biotic development because it involves proteins interacting with the nucleic acids much earlier in evolution than previously suggested. It is even possible that the first self-replicating RNA molecules evolved in association with protein/amyloid and never existed in isolation. An advantage of this model is that it suggests simple evolutionary paths from amyloid-associated elongase and replicase activities to ribosomes and RNA polymerase respectively. In particular, the elongase activity could act as a focus for incremental selective changes that were necessary for the development of template-directed peptide bond formation, without any one step being contingent on future evolutionary developments (Chapple et al., 2003; Huang et al., 2000; Johnston et al., 2001; Lohse and Szostak, 1996; Nissen et al., 2000; Yarus and Welch, 2000; Zhang and Cech, 1997).

A primordial peptide cycle involving the chemical formation and degradation of peptides has recently been proposed (Huber et al., 2003). Here I argue that peptides in solution would be selectively degraded by comparison to those included in amyloid. Mixed chiral peptides are unlikely to have formed amyloid since they have a lower propensity to form -sheet structures (Brack and Barbier, 1990), thus it is likely that amyloid was homochiral and that mixed chiral peptides were selectively degraded and recycled into other random chiral combinations. Base-pairing of nucleic acids during replication has also been argued to promote homochirality (Schoning et al., 2000), leading to the proposal here that both protein and nucleic acid polymers involved in the proposed mechanism were homochiral.There is no a priori reason to believe that any particular homochiral amyloid-nucleic acid combinations (e.g. DD, DL, LD or LL) would have had a selective advantage. Indeed RNA was found to induce the aggregation of both homo L and D poly (Lys-Leu) polypeptides with equal efficiency (Brack and Barbier, 1990). It is therefore possible that all chiral combinations co-existed and competed with each other. The later development of enzymic activities that could direct the synthesis of chiral protein and RNA precursors would then have been the key event in the genesis of the current chiral combination.

The energy itself cannot create them.