Abiogenesis: The formation of life from non-life
Introduction
Evolution comprises the processes whereby life emerged and developed into its present forms over the millions of years [1]. Metabolism and replication are essential for biological life and all biological life has both properties. For replication, enzymes (proteins), RNA and DNA are needed for the successful replication of a cell and the metabolism provides the energy for the process. The chance that both systems arose simultaneously in prebiotic conditions is essentially zero (see creationist calculations).
Peer-reviewed life-origin literature presupposes that, given enough time, genetic instructions arose via natural events, however, no paper has provided a plausible mechanism for natural-process algorithm-writing [2]. Only 200 million years separated the end of Earth’s bombardment from the presumed first appearance of life on Earth 3.8 billion years ago [3,4]. In 200 million years the following has to happen:
From Trevors and Abel (2004) [2].
(1) a genetic operating system with which to record programming instructions,
(2) the programs themselves for production or assembly of every individual building block, biochemical pathway, and metabolic cycle needed for even the simplest protometabolism to develop, and
(3) a coding system with which to translate triplet codon ‘‘language’’ into polyamino acid language.
Current models
1) Protein world first: self-replicating proteins capable of setting up metabolism e.g. kinases.
2) RNA world first
3) Metabolome first
1) Protein world first: self-replicating proteins capable of setting up metabolism e.g. kinases.
The Miller-Urey experiment and other similar experiments are the champions of this hypothesis, showing that the formation of certain amino acids is possible in pre-biotic conditions. In the experiments, a maximum of 2% of the reaction contained amino acids, the majority being glycine and alanine [5]. Less than half of the 20 amino acid required for life were produced [5]. Synthesis of the other amino acids requires much more complex synthesis conditions, mostly unrealistic pre-biotic conditions. Hulett HR (1969) calculated how many molecules could result under ideal conditions, and found that the most abundant amino acids (glycine and alanine) would not have exceeded .0001 gram per liter [6] . This is too dilute to be involved in polymeric reactions required to make proteins
The amino acid composition in these reactions is hetero-chiral. The emergence of homochirality can theoretically become spontaneous in adequate, far-from-equilibrium systems, but only in the presence of energy flows [7]. Whether these “adequate systems” were present in prebiotic condition is unknown and experiments are needed to prove it is even possible.
Assuming that enough amino acids were present in the primordial soup, what next? Amino acids polymerize to form polypeptides and proteins with the help of mRNA, tRNA, peptidyl transferases and ribosomes under very specific pH, temperature and osmotically regulated conditions within a cell. Under preobiotic conditions, some sort of catalyst is needed to facilitate peptide-bond formation in water.
Chessari et al. (2006) described an experimental procedure to mimic the formation of 44 peptide long cooligopetide sequences in many identical copies which may have occurred in the prebiotic molecular evolution [8]. However, the synthesis of the peptides fragments used in the experiment where synthesized based on the Merrifield solid-phase synthesis of peptides, hardly prebiotic plausible scenarios.
But let’s suppose polymerization is not a problem. We find a peptide sequence that is capable of efficiently amplifying homochiral products from a racemic mixture of peptide fragments through a chiroselective autocatalytic cycle. The Ghadiri protein [9]. How was this achieved? A pool of two peptides, one 17 amino acids long and the other is 15 amino acids was added to a controlled mixture
Sequences:
arg-met-lys-gln-lys-glu-glu-lys-val-tyr-glu-lys-lys-ser-lys-val-ala
cys-leu-glu-tyr-glu-val-ala-arg-leu-lys-lys-leu-val-gly-glu
The peptide sequences need to be exact for the experiment to work, otherwise no replication will occur. A constant supply of the two specific peptide sequences was added to the experiment. Every possible strategy of interference was employed by the investigator to promote replication. What are the odds of forming a pool of peptides of this length with those exact sequences in a prebiotic environment, all in a close vicinity to each other and simultaneously considering the following?
Chemical Stability
Chemical Reactivity
Chemical Selectivity
The protein world has its problems.
2) RNA world first
RNA molecules may occasionally, like DNA, store biological information for replication such as the polio or measles viruses, which have an RNA genome. However, this does not happen in living cells, which have a DNA genome. Walter Gilbert formulated the model of an RNA world, a hypothetical stage in the development of life in which DNA and proteins were still both absent and their functions were performed by RNA molecules [10]. It was suggested and is generally the accepted hypothesis that RNA preceded DNA in the origin of life until DNA came on the scene and took over. In this model, the protein-synthesizing machinery e.g. ribosomes, peptidyl transferases and mRNA and tRNA (both RNA molecules) consisted originally of RNA molecules. Therefore the protein components of the protein-synthesizing machinery came after the RNA protein-synthesizing machinery became functional. Most investigators in the development of life contend that RNA preceded protein [11].
Therefore, the appearance of the first RNA molecules represents the central problem posed by the origin of life from an RNA first world perspective. Alas, the prebiotic synthesis of RNA remains unelucidated. Prebiotic synthesis of RNA must give rise to an RNA molecule capable to catalyze the synthesis of molecules of its own kind. This phenomenon has never been observed in nature or, even, in the most ingenious laboratory condition. Scientists are beginning to think that RNA may be too complex to have arisen as the first information-bearing molecule and that it may have been preceded by a simpler organic compound, however no candidates of such a molecule have been detected in present-day organisms [11].
So is the unlikelihood for this model, that we are dangerously near the situation which natural processes cannot account by themselves for the observed phenomena and the intervention of “something else” must be invoked, however scientists feel there is as yet no compelling need for such an attitude [11].
3) Metabolome first
The protein first and RNA first world models are essentially “replication-first” models. The metabolism-first model considers that replication-first models could not have arisen until molecules needed for the replication process had accumulated, with a metabolism based either on simple prebiotic organic molecules or on inorganic carbon sources such as CO2. For a review see Anet (2004) [12]. Metabolic cycles, as they occur in present living cells, have not been demonstrated outside cells and in the absence of enzymes and Anet’s (2004) and Pross’ (2004) analyses concluded that metabolism-first theories are not ‘robust’ or to be recommended over replication first models [12,13]
Origin of the genetic code
It is evident that there is an immense gap from prebiotic chemistry and the lifeless Earth to a complex DNA instruction set containing translational machinery to decode the DNA information. The argument has been repeatedly made that given sufficient time, a genetic instruction set and language system could have arisen. All that would be needed would be diversification, environmental selection, and continuing optimization. But extended time does not provide an explanatory mechanism for spontaneously generated genetic instruction. What is needed is a plausible mechanism for natural-process-generation of functional algorithms. We need empirical evidence of prescriptive genetic information arising spontaneously, without artificial investigator selection and amplification. A fulfilled prediction of the latter would be ideal. So far, none has occurred [2].
The above prebiotic chemistry problems pale in comparison to the difficulty of explaining the origin of (1) an operating system, (2) genetic programming, and (3) encryption/ decryption coding [2]. Natural processes, mechanisms, and chemical catalyses do not explain any of these emergent conceptual phenomena [2].
Contentions that offer nothing more than long periods of time offer no mechanism of explanation for the derivation of genetic programming [2]. No new information is provided by such tautologies. The argument simply says it happened.
As such, it is nothing more than blind belief [2].
Originally Posted by cyghost
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