Conversations with Dimiter Kunnev about the Ribosomehttps://reasonandscience.catsboard.com/t1661p25-translation-through-ribosomes-amazing-nano-machines#8008
In reply to my emailHow ribosomes are like Russian dollshttps://reasonandscience.catsboard.com/t1661-translation-through-ribosomes-amazing-nano-machines#8006
Dimiter Kunnev did send me following reply:
Hi guys, please note that in order for Ribosome to function as protein synthesis needs only PTC even in a primitive form and something to hold it. I'm sending several papers to consider. The entire concept for the irreducibly complex ribosome is only wishful thinking. Enjoy
It is nice first to read the papers and then give answers. From your answer, it is clear that you don't know what you are talking about. Here is the evidence that in order to have peptide synthesis you need only short RNA. Also, I'm sending the 2012 and 2016 Anolles papers where is presented IN DETAILS loop by loop, helix by helix entire evolution of the ribosome. You can see that the ribosomal RNA and tRNA are coevolved EXACTLY as suppose to be according to step by step evolutionary development. ALL DATA CLEARLY SUGGESTS THAT THE RIBOSOME IS NOT IRREDUCEBLY COMPLEX. Your hypothesis for SUDDEN ID dependent formation is NOT supported at all. Please do not answer unprepared and after all, please acknowledge the data even that contradicts your view.
Following science papers were annexed in the first reply:Ribosomal proteins as documents of the transition from unstructured (poly)peptides to folded proteins
https://www.sciencedirect.com/science/article/pii/S1047847717300606Peptidyl-transferase ribozymes: trans reactions, structural characterization and ribosomal RNA-like features
https://www.sciencedirect.com/science/article/pii/S1047847717300606 Could a Proto-Ribosome Emerge Spontaneously in the Prebiotic World?
https://europepmc.org/article/med/27941673History of the ribosome and the origin of translation
https://www.pnas.org/content/112/50/15396Here my reply & comments:Claim: in order for Ribosome to function as protein synthesis needs only PTC even in a primitive form Reply: The Ancient History of Peptidyl Transferase Center Formation as Told by Conservation and Information Analyses
The PTC region has been considered crucial in the understanding about the origins of life
. It has been described as the most significant trigger that engendered a mutualistic behavior between nucleic acids and peptides, allowing the emergence of biological systems.Mutational characterization and mapping of the 70S ribosome active site
03 February 2020
The ribosome's active site accurately and efficiently processes α-amino acid monomers using catalytic rRNA, that we would expect to exhibit high levels of conservation and would be less permissible, or flexible, to mutation.
In fact, previous work has demonstrated in vivo that many nucleotide changes to highly-conserved nucleotides are detrimental
, but the ribosome can still withstand some changes at select positions
As expected, the entire PTC active site (PTC-ring, A-loop, and P-loop) exhibited a high-level of conservation, with ∼75% of the nucleotide positions possessing a Shannon Entropy value at or near zero. My comment:
This is hard evidence, that a stepwise, gradative evolution of the Peptidyl Transferase Center is not supported by the empirical data provided in this paper. Claim:
The emergence of this proto-PTC is a prerequisite to couple a chemical symbiosis between RNAs and peptides that further evolved both to (i) become the large subunit of the ribosome by the principle of accretion and (ii) to allow the emergence of the genetic code. Its importance cannot be challenged as it composes the central core of the decoding language of biology.Reply:
There is no selection pressure why this highly complex system would/should emerge without the genetic code, and vice versa. Claim:
Caetano-Anollés and Sun used structural analyses to provide evidence that tRNAs were older than ribosomes and were coopted to operate in the translation machinery.Reply:
Before the translation machinery can operate, ALL essential players must be fully formed an in place. In the same sense, as an automobile can only fulfill its function, if all parts are working together once fully formed, constituting a device of integrated complexity, the same is the case for the ribosome, where , if even one tiny peace is missing, nothing goes. Imagine, you have a fully operational translation machinery, and instead of all aminoacyl tRNA synthetases are present, what would happen? The entire translation process would absolutely brake down, and any polypeptide product would be non-functional, and not fold into functional 3D forms. Claim:
Farias et al. reconstructed a 3D structure of the PTC based on an ancestral sequence of tRNAs and observed a structural similarity of 92% when compared to the PTC of the bacteria Thermus thermophilus. Together, all these data make evident a scenario for the origin of life in which an evolutionary and chronological connection can be observed between these two essential components of the translation system: tRNAs and rRNAs.Reply:
This makes no sense whatsoever. How do they make the jump from the evidence to the conclusion? How would PTC and tRNA's come to a functional relationship and organization without all other players in place, and the genetic code set up? Observation:
Besides, as we were interested in understanding the relevance of the PTC to the early origin of life, we decided to exclude eukaryotic sequences from the analyses. Eukaryotes are now known to have originated from archaeal organisms coming from the phylum Lokiarchaeota, subphylum Asgard, therefore being derivate clades and having no substantial role in early origins of life Reply:
The authors implicitly admit that there is no homologous sequence of the eukaryotic and prokaryotic ribosome. This is a deal killer form common ancestry ( and there are many other points relevant to this observation, listed later )Claim:
The entire concept for the irreducibly complex ribosome is only wishful thinking. From your answer, it is clear that you don't know what you are talking about. Here is the evidence that in order to have peptide synthesis you need only short RNA. Also, I'm sending the 2012 and 2016 Anolles papers where is presented IN DETAILS loop by loop, helix by helix entire evolution of the ribosome. You can see that the ribosomal RNA and tRNA are coevolved EXACTLY as suppose to be according to step by step evolutionary development. ALL DATA CLEARLY SUGGESTS THAT THE RIBOSOME IS NOT IRREDUCEBLY COMPLEX. Your hypothesis for SUDDEN ID dependent formation is NOT supported at all. Please do not answer unprepared and after all, please acknowledge the data even that contradicts your view.Response:
Handwaving the claim away and glossing over will not solve the point in question, and refute the made observation. If abiogenesis researchers want to be taken seriously, they need to address the objections in a consistent manner, and if a threshold is reached, where natural mechanisms don't suffice, or conceptual problems are pointed out that cannot be overcome, than it is expected that they acknowledge the status quo, and the facts presented. Observing and reasoning about the many intricate patterns in nature requires that one is able to recognize the boundaries of what unguided, random, non-intelligent mechanisms can achieve, and when complexity is observed in the natural world that implodes that range, design should be expected to be inferred as the more case adequate explanation. As we see today, science is unravelling more and more biomechanical complexity, and multilayered information systems working conjoined and in a teamwork. Unfortunately, as it seems, rarely evolutionary biologists are open-minded enough to do so because evolutionary scenarios are ingrained in their thinking from young age and through education, so giving a second thought on the matter is usually not on the table, but evolutionary assertions are asserted over and over, and considered as the only viable and acceptable scenario, while intelligent design is derisen and ridiculed as unscientific, and incredulity is in most cases the only answer.
Fact remains, that translation ONLY works with all parts involved working in an integrated fashion together, in a joint venture.
According to Darwins Theory, the mechanism of natural selection is survival of the fittest. Leaving the fact on side, that there was no life when the Ribosome emerged, ( life depends on the ribosome, andself-replication), the question is:
1. What function would each of the following molecules have on their own?
1. The Ribosome
Conserved nucleotides in the peptidyl-transferase center (PTC) and its proximity may play a key role
in peptide-bond formation
2. Aminoacyl -tRNA synthetases
5. A SELECTED pool of 20 amino acids ( as used in life, from hundreds supposedly existing on early earth )
The functionality of translation would not be maintained after any of the listed parts have been removed. I would go a step further and say, that even changing a few amino acids or ribonucleotides near the peptidyl transferase center, and the entire translation system would absolutely break down. Claim:The Origin of Prebiotic Information System in the Peptide/RNA World: A Simulation Model of the Evolution of Translation and the Genetic Code
2019 Mar 1
This endosymbiosis led to the hierarchical emergence of several requisite components of the translation machine: transfer RNAs (tRNAs), aminoacyl-tRNA synthetase (aaRS), messenger RNAs (mRNAs), ribosomes, and various enzymes. When assembled in the right order, the translation machine created proteins, a process that transferred information from mRNAs to assemble amino acids into polypeptide chains.Response:
How is this not a made-up just so hypothetical scenario that has no real world plausiblity? Why should unguided events lead to hiearchies and emergence at all, rather than racemisation and asphaltization of molecules? The thing is, there's no driver for any of the pieces to evolve individually because single parts confer no advantage in and of themselves.
Assembling things in the right order leading to functional integrated machine-like complexity, where
why would any natural unguided events come up with any of the four molecules, if individually, there would be no function whatsoever for them ? This cannot be pointed out clear enough.
Soren Lovtrup, professional biologist in Sweden, said
"...the reasons for rejecting Darwin's proposal were many, but first of all that many innovations cannot possibly come into existence through accumulation of many small steps, and even if they can, natural selection cannot accomplish it, because incipient and intermediate stages are not advantageous."Natural selection would not select for components of a complex system that would be useful only in the completion of that much larger system.In other words : Why would natural selection select an intermediate biosynthesis product, which has by its own no use for the organism, unless that product keeps going through all necessary steps, up to the point to be ready to be assembled in a larger system ? Never do we see blind, unguided processes leading to complex functional systems with integrated parts contributing to the overall design goal.A minimal amount of instructional complex information is required for a gene to produce useful proteins. A minimal size of a protein is necessary for it to be functional. Thus, before a region of DNA contains the requisite information to make useful proteins, natural selection would not select for a positive trait and play no role in guiding its evolution.
But on top of that: The Ribosome requires over 200 scaffold proteins, chaperones, and 75 cofactors for its assembly. tRNA's also require a very complex biosynthesis pathway. Arguing that natural stepwise, gradual unguided processes produced all these molecular machines resulting in the making of the ribosome which cannot function unless all other parts are there and interconnected, is far from being a reasonable, plausible, and logical assertion and inference.
Translation is just a small part of the entire irreducible chain to make functional proteins: Each individual of the 25 unimaginably complex holoproteins have only function when everything works together:The interdependent and irreducible structures required to make proteinshttps://reasonandscience.catsboard.com/t2039-the-interdependent-and-irreducible-structures-required-to-make-proteins
To make proteins, and direct and insert them to the right place where they are needed, at least 25 unimaginably complex biosyntheses and production-line like manufacturing steps are required. Each step requires extremely complex molecular machines composed of numerous subunits and co-factors, which require the very own processing procedure described below, which makes its origin an irreducible catch22 problem:
THE GENE REGULATORY NETWORK "SELECTS" WHEN, WHICH GENE IS TO BE EXPRESSED
INITIATION OF TRANSCRIPTION BY RNA POLYMERASE
TRANSCRIPTION ERROR CHECKING BY CORE POLYMERASE AND TRANSCRIPTION FACTORS
POLYADENYLATION AND TERMINATION
EXPORT FROM THE NUCLEUS TO THE CYTOSOL
INITIATION OF PROTEIN SYNTHESIS (TRANSLATION) IN THE RIBOSOME
COMPLETION OF PROTEIN SYNTHESIS
PROTEIN TARGETING TO THE RIGHT CELLULAR COMPARTMENT
ENGAGING THE TARGETING MACHINERY BY THE PROTEIN SIGNAL SEQUENCE
CALL CARGO PROTEINS TO LOAD/UNLOAD THE PROTEINS TO BE TRANSPORTED
ASSEMBLY/DISASSEMBLY OF THE TRANSLOCATION MACHINERY
VARIOS CHECKPOINTS FOR QUALITY CONTROL AND REJECTION OF INCORRECT CARGOS
TRANSLOCATION TO THE ENDOPLASMIC RETICULUM
POSTRANSLATIONAL PROCESS OF PROTEINS IN THE ENDOPLASMIC RETICULUM OF TRANSMEMBRANE PROTEINS AND WATER-SOLUBLE PROTEINS
GLYCOSILATION OF MEMBRANE PROTEINS IN THE ER ( ENDOPLASMIC RETICULUM )
ADDITION OF OLIGOSACCHARIDES
INCORRECTLY FOLDED PROTEINS ARE EXPORTED FROM THE ER, AND DEGRADED IN THE CYTOSOL
TRANSPORT OF THE PROTEIN CARGO TO THE END DESTINATIONS AND ASSEMBLYClaim:
Add a part. Make it necessary. That is the heart of Mullerian two-step process.Reply: Müller introduced this concept way back in 1918
, and did so in the following scientific paper: Genetic Variability, Twin Hybrids and Constant Hybrids in a Case of Balanced Lethal Factors by Hermann Joseph Müller, Genetics, 3(5): 422-499 (1918)Here is the relevant quote :Most present-day animals are the result of a long process of evolution, in which at least thousands of mutations must have taken place. Each new mutant in turn must have derived its survival value from the effect upon which it produced upon the 'reaction system' that had been brought into being by the many previously formed factors in cooperation; thus, a complicated machine was gradually built up whose effective working was dependent upon the interlocking action of very numerous different elementary parts or factors, and many of the characters and factors which, when new, were originally merely an asset finally became necessary. Reply: The problem is always explaining how biological information or function is built up in the first place.First paper linked in the email by Dimiter: Ribosomal proteins as documents of the transition from unstructured (poly)peptides to folded proteinsAs a first part of my reply, here to the lucid parts of the paper which partially agree with: Observation:
Most peptides, even those composed of the 20 proteinogenic amino acids, are of no structural and functional use to RNA, placing a premium on synthesizing only useful forms and passing the information on to the next generation. Given the broad spectrum of steps needed to fulfill even the basic requirements of an information-bearing chemical system capable of autocatalytic replication, it seems clear that the RNA-peptide world must have achieved considerable complexity well before its transition to the DNA-protein world we observe today. In making this transition, the RNA-peptide world faced a considerable challenge: whereas the chemistry of the RNA-to-DNA transition seems unproblematic (Ritson and Sutherland, 2014), there is a major obstacle on the path from peptides to proteins, known as the protein folding problem.Reply: Origin and Evolution of DNA and DNA Replication Machineries
Scientists are struggling to answer major questions such as: how did the DNA/Protein world come about, why would such partition of tasks evolve in the RNA world, and which came first, DNA or Protein? Again, we find the ‘chicken and egg’ problem.
Ribonucleotide reductase (RNR) which are the main player in the transition from RNA to DNA are ENORMOUSLY COMPLEX proteins. It takes these enzymes to make DNA. But it takes DNA to make these enzymes. What came first? From RNA to DNA impossiblehttps://reasonandscience.catsboard.com/t1784-from-rna-to-dna-impossibleFormation of Deoxyribonucleotideshttps://reasonandscience.catsboard.com/t2028-the-dna-double-helix-evidence-of-design#3432The protein folding problem from an evolutionary perspective
Protein structure, in contrast, is an altogether more complex property and the process by which proteins reach their structure (folding) is easily disrupted and readily undone by even minor changes in temperature or the chemical environment.
Once denatured, proteins tend to aggregate and can either not be renatured, or only with large loss of material, making denaturation a substantially irreversible process. The easy loss of structure in most proteins is due to the low free energy of folding (often equivalent to just a few hydrogen bonds), which places them energetically close to the unfolded state. Their tendency to aggregate upon denaturation is due to the dominant role of the hydrophobic effect in folding, which leads folded proteins to mainly segregate hydrophobic residues to the protein core and hydrophilic residues to the surface. When the hydrophobic residues of the core become exposed in the denatured state, they tend to coalesce into heterogeneous tangles, which are generally impossible to resolve and must be degraded. The closeness of the structured and unstructured states in most proteins and the many problems arising to living beings from this are documented in the elaborate protein quality control and degradation systems that are universal to lifeForces Stabilizing Proteins - essential for their correct foldinghttps://reasonandscience.catsboard.com/t2692-forces-stabilizing-proteins-essential-for-their-correct-foldingEven biophotons!! are involved in protein folding: The mechanism and properties of bio-photon emission and absorption in protein molecules in living systems
https://aip.scitation.org/doi/10.1063/1.4709420Quantum mechanic communication in cells: A paradigm shift in biologyhttps://www.youtube.com/watch?v=9x32MF79AkAhttps://reasonandscience.catsboard.com/t3021-awe-inspiring-biophoton-cell-cell-communication-points-to-design#7981Claim:
Proteins from peptides: The staggering size of protein sequence space and the low incidence of folded exemplars within it essentially preclude an origin of folded domains by random concatenation of amino acids.
An alternative scenario proposes that the first folded domains did not arise from random processes, but from the increased complexity of the peptides that had evolved in the RNA worldReply:
This is an entirely UNSUPPORTED claim. No evidence that RNA molecules ever had the broad range of catalytic activitieshttps://reasonandscience.catsboard.com/t2243-no-evidence-that-rna-molecules-ever-had-the-broad-range-of-catalytic-activitiesThe origin of replication and translation and the RNA Worldhttps://reasonandscience.catsboard.com/t2234-the-origin-of-replication-and-translation-and-the-rna-world
The replicase itself is produced by translation of the respective mRNA(s), which is mediated by the immensely complex ribosomal apparatus. Hence, the dramatic paradox of the origin of life is that, to attain the minimum complexity required for a biological system to start on the Darwin-Eigen spiral, a system of a far greater complexity appears to be required.
How such a system could evolve is a puzzle that defeats conventional evolutionary thinking, all of which is about biological systems moving along the spiral; the solution is bound to be unusual. Claim:
For the most part, contemporary proteins can be traced back to a basic set of a few thousand domain prototypes, many of which were already established in the Last Universal Common Ancestor of life on Earth, around 3.5 billion years ago. Response: Common descent, the tree of life, a failed hypothesishttps://reasonandscience.catsboard.com/t2239-evolution-common-descent-the-tree-of-life-a-failed-hypothesis1. The DNA replication machinery is not homologous in the 3 domains of life. The bacterial core replisome enzymes do not share a common ancestor with the analogous components in eukaryotes and archaea.2. Bacteria and Archaea differ strikingly in the chemistry of their membrane lipids. Cell membrane phospholipids are synthesized by different, unrelated enzymes in bacteria and archaea, and yield chemically distinct membranes.3. Sequences of glycolytic enzymes differ between Archaea and Bacteria/Eukaryotes. There is no evidence of a common ancestor for any of the four glycolytic kinases or of the seven enzymes that bind nucleotides.4. There are at least six distinct autotrophic carbon fixation pathways. If common ancestry were true, an ancestral Wood–Ljungdahl pathway should have become life's one and only principle for biomass production.5. There is a sharp divide in the organizational complexity of the cell between eukaryotes, which have complex intracellular compartmentalization, and even the most sophisticated prokaryotes (archaea and bacteria), which do not.6. A typical eukaryotic cell is about 1,000-fold bigger by volume than a typical bacterium or archaeon, and functions under different physical principles: free diffusion has little role in eukaryotic cells but is crucial in prokaryotes7. Subsequent massive sequencing of numerous, complete microbial genomes have revealed novel evolutionary phenomena, the most fundamental of these being: pervasive horizontal gene transfer (HGT), in large part mediated by viruses and plasmids, that shapes the genomes of archaea and bacteria and call for a radical revision (if not abandonment) of the Tree of Life concept8. RNA Polymerase differences: Prokaryotes only contain three different promoter elements: -10, -35 promoters, and upstream elements. Eukaryotes contain many different promoter elements9. Ribosome and ribosome biogenesis differences: Although we could identify E. coli counterparts with comparable biochemical activity for 12 yeast ribosome biogenesis factors (RBFs), only 2 are known to participate in bacterial ribosome assembly. This indicates that the recruitment of individual proteins to this pathway has been largely independent in the bacterial and eukaryotic lineages. 22Observation:
The origin of these domain prototypes, however, remains poorly understood.Response: Uncertainty quantification of a primordial ancestor with a minimal proteome emerging through unguided, natural, random eventshttps://reasonandscience.catsboard.com/t2508-abiogenesis-uncertainty-quantification-of-a-primordial-ancestor-with-a-minimal-proteome-emerging-through-unguided-natural-random-eventsThe simplest free-living bacteria is Pelagibacter ubique. 13 It is known to be one of the smallest and simplest, self-replicating, and free-living cells. It has complete biosynthetic pathways for all 20 amino acids. These organisms get by with about 1,300 genes and 1,308,759 base pairs and code for 1,354 proteins. 14 That would be the size of a book with 400 pages, each page with 3000 characters. They survive without any dependence on other life forms. Incidentally, these are also the most “successful” organisms on Earth. They make up about 25% of all microbial cells. If a chain could link up, what is the probability that the code letters might by chance be in some order which would be a usable gene, usable somewhere—anywhere—in some potentially living thing? If we take a model size of 1,200,000 base pairs, the chance to get the sequence randomly would be 4^1,200,000 or 10^722,000. Claim:
One hypothesis posits that they arose from an ancestral set of peptides, which acted as cofactors of RNAmediated catalysis and replication.Response: (Big!)problem 1: New technologies to analyse protein function: an intrinsic disorder perspective
The corresponding DNA sequences dictate the amino acid sequences. Specific functionality of a given protein is defined by a unique spatial positioning of its amino acid side chains and prosthetic groups, suggesting that such a specific spatial arrangement of functional groups in biologically active proteins is defined by their unique 3D structures predetermined by the unique amino acid sequences encoded in unique genes.Basic molecules need to polymerize to become information-bearing genomes and proteins with specific functions and come into a functional relationship and interdependence. An organizational structure would have to be established between the domain of information and computation ( the genome and epigenetic information orchestrating gene expression ) and the mechanistic domain, where proteins and enzymes work based on the direction and information flow of the beforementioned blueprint-like information. The puzzle lies with the problem of creating a causal organization, the interrelationship of informational and mechanical aspects into interdependent narratives. One of the challenges of life’s origin is thus to explain how instructional information control systems emerge naturally and spontaneously from mere chemical interactions and start taking over the clever making and control of molecular mechanical dynamics. In modern cells, to make proteins, at least 25 unimaginably complex biosyntheses and production-line like manufacturing steps through large multimolecular machines are required. Each step requires exquisitely engineered molecular machines composed of an enormous number of subunits and co-factors, which require the very own processing procedure described, which makes its origin an irreducible catch22 problem.Problem 2: Peptide Bond Formation of amino acids in prebiotic conditions: another unsurmountable problem of protein synthesis on early earthhttps://reasonandscience.catsboard.com/t2130-peptide-bonding-of-amino-acids-to-form-proteins-and-its-origins#6664The Role of Lipid Membranes in Life’s Origin
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5370405/A plausible mechanism for synthesis of peptide bonds and ester bonds on the prebiotic Earth continues to be a major gap in our understanding of the origin of life.Peptides by Activation of Amino Acids with CO on (Ni,Fe)S Surfaces: Implications for the Origin of LifeClaudia Huber and Guenter WaechtershaeuserUnder the dilute aqueous conditions most relevant for the origin of life, activation of the amino acids by coupling with hydrolysis reactions notably of inorganic polyphosphates has been suggested. It is, however, not clear how underhot aqueous conditions such hydrolytically sensitive coupling compounds, if geochemically available at all, could resist rapid equilibration.http://fire.biol.wwu.edu/cmoyer/zztemp_fire/biol345_S99/huber2.pdfProblem 3: the prevalence of protein sequences adopting functional enzyme folds.
Combined with the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10(77)
, adding to the body of evidence that functional folds require highly extraordinary sequences.
https://www.ncbi.nlm.nih.gov/pubmed/15321723?fbclid=IwAR2WqQIOoD3Opw1tmhd6Z5K76yAcJ-w_DbwlWnPml5jVxM34YxC9l7N3PHwChemical evolution of amino acids and proteins ? Impossible !! https://reasonandscience.catsboard.com/t2887-chemical-evolution-of-amino-acids-and-proteins-impossibleClaim:
Initially, these peptides were entirely dependent on the RNA scaffold for their structure, but as their complexity increased, they became able to form structures by excluding water through hydrophobic contacts, making them independent of the RNA scaffold.Reply:
How does the author know that there were RNA scaffolds on prebiotic earth?Claim:
ability to fold was thus an emergent property of peptide-RNA coevolution. The ribosome is the main survivor of this primordial RNA world and offers an excellent model system for retracing the steps that led to the folded proteins of today, due to its very slow rate of change. Close to the peptidyl transferase center, which is the oldest part of the ribosome, proteins are extended and largely devoid of secondary structure; further from the center, their secondary structure content increases and supersecondary topologies become common, although the proteins still largely lack a hydrophobic core; at the ribosomal periphery, supersecondary structures coalesce around hydrophobic cores, forming folds that resemble those seen in proteins of the cytosol. Collectively, ribosomal proteins thus offer a window onto the time when proteins were acquiring the ability to fold.Reply:
These are unsupported claims. Observation: It seems impossible that this elaborate interplay of complex macromolecules could have emerged de novo from abiotic processesReply:
ABSOLUTELY AGREED. Claim:
it is generally accepted that life must have started in a simpler form, which has been the subject of much theorizing and some experimentation. Among the possibilities considered, by far the most popular and best supported has been that of RNA forming the first systems capable of autocatalytic replication, acting as both the information bearer and the agent of catalysis. The RNA world is now well established and
widely considered to have been the direct precursor to the DNAprotein world of today.Reply: The problem of the origin of the hardware and software in the cell is far greater than commonly appreciatedhttps://reasonandscience.catsboard.com/t2997-the-problem-of-the-origin-of-the-hardware-and-software-in-the-cell-is-far-greater-than-commonly-appreciatedThe very origin of the first organisms presents at least an appearance of a paradox because a certain minimum level of complexity is required to make self-replication possible at all; high-fidelity replication requires additional functionalities that need even more information to be encoded. The crucial question is how the Darwin-Eigen cycle could have started—how was the minimum complexity that is required to achieve the minimally acceptable replication fidelity attained? In even the simplest modern systems, such as RNA viruses, replication is catalyzed by complex protein polymerases. The replicase itself is produced by translation of the respective mRNA(s), which is mediated by the immensely complex ribosomal apparatus. Hence, the dramatic paradox of the origin of life is that to attain the minimum complexity required for a biological system to start on the Darwin-Eigen spiral, a system of a far greater complexity appears to be required. How such a system could emerge is a puzzle that defeats conventional evolutionary thinking, all of which is about biological systems moving along the spiral; the solution is bound to be unusual. The origin of life—or, to be more precise, the origin of the first replicator systems and the origin of translation—remains a huge enigma, and progress in solving these problems has been very modest—in the case of translation, nearly negligible.4Second paper linked in the email by Dimiter: Peptidyl-transferase ribozymes: trans reactions, structural characterization and ribosomal RNA-like features Claim:
Similar catalytic rates but different primary sequences and different metal ion requirements. One of these ribozymes has now been re-engineered
to catalyze intermolecular peptide-bond formation using an aminoacylated nucleotide and an amino-acid-linked oligonucleotide as substrates. Our results demonstrate that a ribozyme can catalyze peptide-bond formation reactions analogous to the action of the ribosome and, most surprisingly, appears to use similar sequence and structure motifs. These findings provide evidence for the feasibility of the Reply:
The authors confess re-engineering. That means ===>>> Intelligent design !! Case closed. Third paper linked in the email by Dimiter:Could a Proto-Ribosome Emerge Spontaneously in the Prebiotic World? Observation:
An indispensable prerequisite for establishing a scenario of life emerging by natural processes is the requirement that the first simple proto-molecules could have had a realistic probability of self-assembly from random molecular polymers in the prebiotic world.Reply:
There is more than enough evidence demonstrating that protein synthesis by unguided random events is not possible at all. https://reasonandscience.catsboard.com/t2706-main-topics-on-proteins-and-protein-synthesisClaim:
Three concentric structural elements of different magnitudes, having a dimeric nature derived from the symmetrical region of the ribosomal large subunit, were suggested to constitute the vestige of the proto-ribosome. It is assumed
to have materialized spontaneously
in the prebiotic world, catalyzing non-coded peptide bond formation and simple elongation. Reply: The problem of chain terminationhttps://reasonandscience.catsboard.com/t2130-peptide-bonding-of-amino-acids-to-form-proteins-and-its-originsTo form a chain, it is necessary to react bifunctional monomers, that is, molecules with two functional groups so they combine with two others. If a unifunctional monomer (with only one functional group) reacts with the end of the chain, the chain can grow no further at this end. If only a small fraction of unifunctional molecules were present, long polymers could not form. But all ‘prebiotic simulation’ experiments produce at least three times more unifunctional molecules than bifunctional molecules. Formic acid (HCOOH) is by far the commonest organic product of Miller-type simulations. Indeed, if it weren’t for evolutionary bias, the abstracts of the experimental reports would probably state nothing more than: ‘An inefficient method for production of formic acid is here described …’ Formic acid has little biological significance except that it is a major component of ant (Latin formica) stings.Observation:
Even the sequence of a simple ribozyme of 40 nucleotides has 10^24 possible compositions. To represent all of these compositions at least once, and thus to establish a certainty that this simple ribozyme could have materialized, requires 27 kg of RNA chains, which classifies spontaneous emergence as a highly implausible event.Reply:
We are in FULL AGREEMENT with the observation :=)) Observation:
probability of spontaneous occurrence of the DPR sequence, obtained under the notion of limited sequence specificity, may be too optimistic, but even a significantly lower probability is still acceptable, taking into consideration that the emergence of life is believed to have occurred just once. Given optimal, yet unknown environmental conditions and sufficient time, a small pond with a relatively low concentration of random RNA chains of about 70 mer may have provided feasible likelihood
for the materialization of a prebiotic apparatus catalyzing non-coded peptide-bond formation and simple elongation. Reply:
So what is it now? Highly implausible, or feasible likelihood ? The paper is in contradiction with itself !! Observation:
The first true alternative to terrestrial biology will be found on an extrasolar planet, in a rock from Mars, or within an extreme environment on Earth. More likely, it will be the handiwork of an intelligent species that has discovered the principles of Darwinian evolution and learned to devise chemical systems that have the capacity to generate bits on their own.Reply:
Or maybe a superpowerful intelligent creator was involved ? Seems the most likely scenario to me. Fourth paper provided by Dimiter: History of the ribosome and the origin of translationIntro:
We present a molecular-level model for the origin and evolution of the translation system, using a 3D comparative method. In this model, the ribosome evolved by accretion, recursively adding expansion segments, iteratively growing, subsuming, and freezing the rRNA.Reply:
When naturalistic explanations are short coming, it is not rare that the authors resort ad-hoc to a "frozen accident". The intro of the paper resorts as well to that "escape", and as such, it is a implicit admission that rational evidence based , plausible and logical explanations are lacking. Science-based on materialism resorting to frozen accidents.https://reasonandscience.catsboard.com/t2889-science-based-on-materialism-resorting-to-frozen-accidentsClaim:
Prokaryotic ribosomes evolved in six phases, sequentially acquiring capabilities for RNA folding, catalysis, subunit association, correlated evolution, decoding, energy-driven translocation, and surface proteinization.Reply:
Why should stochastic unguided natural events " evolve" capabilities in a orderly sequenced fashion ? This is streching far too far the capabilities of unguided random chemical reactions!! How is it possible, that the authors are not realizing this VERY OBVIOUS fact? Not only that, but they outline what it is, namely: RNA folding, catalysis, subunit association, correlated evolution, decoding, energy-driven translocation, and surface proteinization. WOW!!! I mean: Really ???!!
I mean: How can the authors make such a huge claim, shamelessly, without a blinker of an eye? This is just ad-hoc speculation without a SHRED of evidence to back up the claims. This is not science. This is PSEUDO-SCIENTIFIC hogwash
!! How can people not realize this?? In regards of the origin of tRNAs: Piecemeal Buildup of the Genetic Code, Ribosomes, and Genomes from Primordial tRNA Building Blockshttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5198078/Claim: tRNA is the oldest and most central nucleic acid molecule of the cell. Its co-evolutionary interactions with aminoacyl-tRNA synthetase protein enzymes define the specificities of the genetic code and those with the ribosome their accurate biosynthetic interpretation.Reply: Why should tRNA's define the genetic code? There is no reason, why unguided events would have selected a set of 20 amino acids, nor their cognate aminoacyl-tRNA synthetases, and even less, that these molecules would have frozen somehow the triplet codon set of RNA's or DNA. Simply said: This is baseless speculation without a shred of evidence to back up the claim. Its a made-up story.Claim: We propose that these nucleic acid loops were capable of interacting stereochemically with evolving protein structure and responding to their molecular makeup.Reply: Claiming that proteins are the product of evolution is unsupported. There is no evidence for this.Claim: Increases in these interactions canalized both the appearance of genetic memory and building blocks (modules) of RNA with which to construct processive biosynthetic machinery on one hand and genomic memory storage on the other.Reply: One of the challenges of life’s origin is thus to explain how instructional information control systems emerge naturally and spontaneously from mere chemical interactions and start taking over the clever making and control of molecular mechanical dynamics.1. Whenever there are things that cohere only because of a purpose or function (for example, all the complicated parts of a watch that allow it to keep time), we know that they had a designer who designed them with the function in mind; they are too improbable to have arisen by random physical processes. (A hurricane blowing through a hardware store could not assemble a watch.)2. The essential parts of a living cell cohere to a functional whole. They are found forming an integrated complex system because they make it possible together for the cell to self-replicate, adapt, and remain alive. There is an organizational structure between the domain of specified complex information that cleverly directs the making all functional parts and controls molecular mechanical dynamics and self-replication.3. The functional organization which makes chemicals, building blocks, and macromolecules must have a designer who designed the system with the function in mind: just as a watch implies a watchmaker, a machine implies a machine designer, and a factory, a factory maker. Living cell factories full of machines made through the instructional genetic information were not created by human designers. Therefore, living cells must have had a non-human intelligent designerTransfer RNA, and its biogenesis, best explained through designhttps://reasonandscience.catsboard.com/t2070-transfer-rna-and-its-biogenesistRNA's are very specific molecules, and the " made of " follows several steps, requiring a significant number of proteins and enzymes, which are often made of several subunits and ainded by essential co-factors and metals.The challenge for evolution to the fact, that biological systems incorporate several essential parts, that cannot be eliminated without losing the core function of the system in question, and that these parts have no function of their own and could therefore not be product of natural mechanisms, of gradual evolutionary steps, is in my view more severe than most philosophers of science and scientists like Behe exemplify. In systems of enormous biological complexity like the cell, thousands of parts are essential , many more parts, than the well known examples like the flagellum. Irreducibility is found from the highest level of biological organisation and systems, to a single DNA deoxyribonucleotide, which loses function if reduced to its single components, the bases, phosphate or sugar. Just take off one, and the molecule loses its function. Same goes for the cell. Take off one building block, like the spindle apparatus, and mitosis and cell division is not possible, and life could not reproduce itself.The make of proteins is similar to the make of cars in a car factory. If the grinder machine to make the motor pistons has a mal function, the pistons cannot be finished, the car's motor block cannot be assembled with all parts, and the motor would not function without that essential part. Amongst thousands of parts, just a tiny one will compromise the function of the whole system. In biological nano-factories, the solutions to overcome problems like damage must all be pre-programmed, and the repair "working horses" to resolve the problem must be ready in place and "know" what to do how, and when. If a roboter in a factory assembly line fails, employees are ready to detect the error and make the repair . In the cell, the mal function of any part even as tiny and irrelevant as it might seem, can be fatal, and if the repair mechanisms are not functioning correctly and fully in place right from the start, the repair can't be done, and life ceases. These repair enzymes which cleave, join, add, replace etc. must be programmed in order to function properly right from the start. Aberrantly processed pre-tRNAs for example are eliminated through a nuclear surveillance pathway by degradation of their 3′ ends, whereas mature tRNAs lacking modifications are degraded from their 5′ends in the cytosol.