I will praise thee; for I am fearfully and wonderfully made: Psalm 139:14
It is argued that the record of changes is held in rRNA secondary and three-dimensional structures. Patterns observed in extant rRNA found among organisms were used to generate rules supposedly governing the changes.
First, it is assumed that evolution occurred with changes moving from prokaryotes leading finally to the eukaryotes and with the apex reached with humans.
Using this framework, a chronological sequence was constructed of rRNA segment additions to the core structure found in Escherichia coli. The six-phase process envisaged provided no evidence for the emergence of ancestral RNA. The proto-mRNA is seen simply as arising from a random population of appropriate molecules.
This proto-mRNA together with tRNA, formed through condensation of a cysteine: cysteine: alanine (CCA) sequence unit, gave rise to base-pair coding triplets (codons). The ribosomal units (small and large) are considered to have arisen from loops of the rRNA. The proposed RNA loops were ‘defect-laden’, which required a protection mechanism.
During phase 2 the large ribosomal unit is thought of as a crude ribozyme almost as soon as it was a recognizable structure, catalyzing nonspecific, non-coded condensation of amino acids. Finally, the two developing ribosome units came together (phase 4) to form a complex structure recognizable as a ribosome. In the next phase (5), specific interactions began to occur between anticodons in tRNA and mRNA codons to produce functional proteins. In the final phase the genetic code was optimized.
This narrative suffers from major flaws, some of which also are inherent in previous models of the genetic code generation.
--No organisms have been found that contain ribosomes in any of these intermediary phases.
--If these intermediary phases are capable of ribosomal function, then why was it necessary to evolve further during additional steps? --An insistent problem is how a genetic code could be generated that depends for its expression on proteins that can only be formed when it exists. Petrov et al. proposed a partial solution. The peptidyl transferase (enzyme) centre, an essential component of the ribosome, arose from an rRNA fragment. This means that its origin is conceived of as being in the RNA world. The peptidyl transferase centre is the place in the 50S LSU where peptide bond synthesis occurs. The machinery is very complex in extant organisms. In its original incarnation, the embryonic centre was less than 100 nucleotides long. The original RNA world quickly morphed into the familiar RNA/protein world. This argument is necessary as it “has proven experimentally difficult to achieve” a self-replicating RNA system. In a revealing aside, Fox even suggested that perhaps it is not necessary to validate the existence of the RNA world if it had a short life.
--However, such enzymes are unable to copy long templates and at a sufficient rate to overtake decomposition processes.
--Even greater issues are that there is no sensible resolution to the question of the origin of the activated nucleotides through abiotic processes needed for RNA formation, or of the problem as to how randomly assembled nucleotides achieved the ability to replicate. This has led some to conclude that “the model does not appear to be very plausible”. Nevertheless, undaunted, other possibilities have been invented." CMI
The accretion model of ribosomal evolution
"The accretion model of ribosomal evolution is one of the most recent models and describes how the ribosome evolves from simple RNA and protein elements into an organelle complex in six major phases through accretion, recursively adding, iterative processes, subsuming and freezing segments of the rRNA.It is argued that the record of changes is held in rRNA secondary and three-dimensional structures. Patterns observed in extant rRNA found among organisms were used to generate rules supposedly governing the changes.
First, it is assumed that evolution occurred with changes moving from prokaryotes leading finally to the eukaryotes and with the apex reached with humans.
Using this framework, a chronological sequence was constructed of rRNA segment additions to the core structure found in Escherichia coli. The six-phase process envisaged provided no evidence for the emergence of ancestral RNA. The proto-mRNA is seen simply as arising from a random population of appropriate molecules.
This proto-mRNA together with tRNA, formed through condensation of a cysteine: cysteine: alanine (CCA) sequence unit, gave rise to base-pair coding triplets (codons). The ribosomal units (small and large) are considered to have arisen from loops of the rRNA. The proposed RNA loops were ‘defect-laden’, which required a protection mechanism.
During phase 2 the large ribosomal unit is thought of as a crude ribozyme almost as soon as it was a recognizable structure, catalyzing nonspecific, non-coded condensation of amino acids. Finally, the two developing ribosome units came together (phase 4) to form a complex structure recognizable as a ribosome. In the next phase (5), specific interactions began to occur between anticodons in tRNA and mRNA codons to produce functional proteins. In the final phase the genetic code was optimized.
This narrative suffers from major flaws, some of which also are inherent in previous models of the genetic code generation.
--No organisms have been found that contain ribosomes in any of these intermediary phases.
--If these intermediary phases are capable of ribosomal function, then why was it necessary to evolve further during additional steps? --An insistent problem is how a genetic code could be generated that depends for its expression on proteins that can only be formed when it exists. Petrov et al. proposed a partial solution. The peptidyl transferase (enzyme) centre, an essential component of the ribosome, arose from an rRNA fragment. This means that its origin is conceived of as being in the RNA world. The peptidyl transferase centre is the place in the 50S LSU where peptide bond synthesis occurs. The machinery is very complex in extant organisms. In its original incarnation, the embryonic centre was less than 100 nucleotides long. The original RNA world quickly morphed into the familiar RNA/protein world. This argument is necessary as it “has proven experimentally difficult to achieve” a self-replicating RNA system. In a revealing aside, Fox even suggested that perhaps it is not necessary to validate the existence of the RNA world if it had a short life.
An RNA commencement to life on Earth rests on the ability of RNA to both share the task of encoding and also to replicate information.
This proposition depends on the abilities of RNA copying enzymes (ribozymes). --However, such enzymes are unable to copy long templates and at a sufficient rate to overtake decomposition processes.
--Even greater issues are that there is no sensible resolution to the question of the origin of the activated nucleotides through abiotic processes needed for RNA formation, or of the problem as to how randomly assembled nucleotides achieved the ability to replicate. This has led some to conclude that “the model does not appear to be very plausible”. Nevertheless, undaunted, other possibilities have been invented." CMI