Defending the Christian Worlview, Creationism, and Intelligent Design
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Defending the Christian Worlview, Creationism, and Intelligent Design
This is my personal virtual library, where i collect information, which leads in my view to the Christian faith, creationism, and Intelligent Design as the best explanation of the origin of the physical Universe, life, and biodiversity
Posts : 6079 Join date : 2009-08-09 Age : 54 Location : Aracaju brazil
Eörs Szathmáry Toward major evolutionary transitions theory 2.0 April 2, 2015 https://www.pnas.org/content/112/33/10104 Origins of Life: Three Early Phases of Transitions to Cells Progress about the origins of life has been considerable although the nut is still hard to crack. New experiments and theoretical insights have been generated, but, equally important, we now have a much better understanding of what we do not understand (moving from “unknown unknowns” to “known unknowns”).
The Origin of the First Hereditary Replicators. This process is still an unsolved problem. By itself, this transition is not an evolutionary one because, without hereditary replicators, no Darwinian evolution is possible. However, we have to consider the gray zone where chemistry and evolution had the first overlap. As Orgel noted: “All replicating systems are, by definition, autocatalytic and all autocatalytic systems result, in some sense, in replication” (ref. 25, p. 203). Transition theory has adopted this view throughout the years, which also led to a new way of classifying replicators.
There is a possibility that autocatalytic macromolecular networks without template replication could exist. Imagine a network of peptides in which some peptides can catalyze the formation of other peptides from amino acids and simpler peptides. Recent calculations show that the probability of formation is higher than previously thought and that there is limited evolvability, provided that reflexively autocatalytic networks are compartmentalized. This option is also compatible with the view that the RNA world may have never been clean and that amino acids and peptides played some important role in the beginning: for example, in the handling of membrane permeability.
There is ample evidence supporting the view that the RNA world in fact existed, but many agree that it may not have been the earliest genetic system, because of difficulties with its origin. Despite recent progress, we still have no general RNA-based replicase that could replicate a great variety of sequences, including copies of its own. I briefly consider novel issues in turn. A potential way out of the missing RNA replicase problem could be a network in which two types of ribozymes act together: replicases replicate short strands that would be linked by ligases. Both ligases and replicases would form in this way. Template effects are important, and the system as a whole is collectively autocatalytic. We have nice examples of a ligase-based anabolic autocatalytic system and a collectively autocatalytic set of minimalist nucleic acid replicators.
The Error Threshold of Molecular Replication and the Maintenance of Integrated Information. Once RNA genes could be mechanistically replicated one way or another, a first appearance of intragenomic conflict arises due to Eigen’s error threshold. Limited replication accuracy in early systems would have allowed the maintenance by selection of single genes only that in turn would have competed with each other.
Posts : 6079 Join date : 2009-08-09 Age : 54 Location : Aracaju brazil
Antonio Lazcano ( AL): ......and that because of our work with the possibility of having an RNA world in the very earliest stages of evolution, we did have the, also the intellectual understanding of the genetics, the structure, the evolution of RNA systems. Reply:Graham Cairns-Smith: The odds against a successful unguided synthesis of a batch of primed nucleotide on the primitive Earth would be a huge number, represented approximately by a 1 followed by 109 zeros ( 10^109). 'The odds are enormous against its being coincidence. No figures could express them.'
1. No prebiotic mechanism is known to select: - Right-handed configurations of RNA and DNA - The right backbone sugar - How to get size complementarity of the nucleotide bases to form a DNA strand and strands of the DNA molecule running in the opposite directions
2.Bringing all the parts together and joining them in the right position - Attach the nucleic bases to the ribose and in a repetitive manner at the same, correct place, and the backbone being a repetitive homopolymer - Prebiotic glycosidic bond formation between nucleosides and the base - Prebiotic phosphodiester bond formation - Fine-tuning of the strength of the hydrogen base pairing forces
3. The instability, degradation, and asphalt problem - Bonds that are thermodynamically unstable in water, and overall intrinsic instability. RNA’s nucleotide building blocks degrade at warm temperatures in time periods ranging from nineteen days to twelve years. These extremely short survival rates for the four RNA nucleotide building blocks suggest why life’s origin would have to be virtually instantaneous—all the necessary RNA molecules would have to be assembled before any of the nucleotide building blocks decayed.
4. The energy problem - Doing things costs energy. There has to be a ready source of energy to produce RNA. In modern cells, energy is consumed to make RNA.
5. The minimal nucleotide quantity problem. - The prebiotic conditions would have had to be right for reactions to give perceptible yields of bases that could pair with each other.
6. The Water Paradox - The hydrolytic deamination of DNA and RNA nucleobases is rapid and irreversible, as is the base-catalyzed cleavage of RNA in water. This leads to a paradox: RNA requires water to do its job, but RNA cannot emerge in water and cannot replicate with sufficient fidelity in water without sophisticated repair mechanisms in place.
7.The transition problem from prebiotic to biochemical synthesis - Even if all this in a freaky accident occurred by random events, that still says nothing about the huge gap and enormous transition that would be still ahead to arrive at a fully functional interlocked and interdependent metabolic network, where complex biosynthesis pathways produce nucleotides in modern cells.
AL: If you simulate the conditions of the primitive word you can actually synthesize in a very rapid time, in a very quick interval of time, you can synthesize amino acids, hydroxides, and so on, thus proving that in principle you could have those organic molecules in the primitive world prior to the origins of life. Reply: Paradoxes in the origin of life. 2015 Jan 22 Benner SA1. http://sci-hub.ren/https://www.ncbi.nlm.nih.gov/pubmed/25608919
We are now 60 years into the modern era of prebiotic chemistry. That era has produced tens of thousands of papers attempting to define processes by which “molecules that look like biology” might arise from “molecules that do not look like biology” …. For the most part, these papers report “success” in the sense that those papers define the term…. And yet, the problem remains unsolved
Chemical evolution of amino acids and proteins ? Impossible !! https://www.youtube.com/watch?v=1L1MfGrtk0A
AL: of people with an extraordinary insight, became fully aware that if you want to have enzyme catalytic activity you require coenzymes and most of the coins are actually ribonucleotide derivatives. Reply:Synthesis of Coenzyme A https://reasonandscience.catsboard.com/t2691-synthesis-of-coenzyme-a In all living organisms, coenzyme A is synthesized in a five-step process that requires four molecules of ATP, pantothenate and cysteine.
It takes enzymes to make co-enzyme A. But you require to Coenzyme A to have enzyme catalytic activity. What came first?
Coenzymes are essential across all domains of life. B vitamins (B1-thiamin, B2- riboflavin, B3-niacin, B5-pantothenate, B6-pyridoxine, B7-biotin, and B12-cobalamin) represent the largest class of coenzymes, which participate in a diverse set of reactions including C1-rearrangements, DNA repair, electron transfer, and fatty acid synthesis.
Consider in special the ENORMOUS problem to get Vitamin B12 prebiotically, which is required in DNA synthesis:
Elucidation of the anaerobic pathway for the corrin component of cobalamin (vitamin B12) September 10, 2013 https://www.pnas.org/content/110/37/14906 The anaerobic route has remained enigmatic because many of its intermediates have proven technically challenging to isolate, because of their inherent instability. The full step-by-step in vitro synthesis of cobyrinic acid from ALA requires 14 enzymes
Nearly all animal life is dependent on bacteria for survival as only bacteria and some archaea possess the genes and enzymes necessary to synthesize vitamin B12, also known as cobalamin, and provide it through the food chain. 1 Vitamin B12, also known as cobalamin, is a water-soluble vitamin involved in the metabolism of every cell of the human body. It is one of eight B vitamins. It is a cofactor in DNA synthesis, and in both fatty acid and amino acid metabolism.
AL: Then in 1960, 1961 RNA was able to synthesize adenine. So you could demonstrate that in the primitive conditions, prebiotic chemistry could lead to the formation of some of the components of DNA and RNA. Reply: That does not correspond to the facts. There are still at least 27 relevant, unanswered questions today in regards of prebiotic synthesis of RNA and DNA:
- Getting the basic elements to make the building blocks of life - RNA world - RNA and DNA synthesis - Polymerization through catalysts on clay - The Eigen threshold - The transition from the RNA world, to the DNA world - Obtaining the genetic Code - The genetic code is optimal amongst 1 million - The second, overlapping code in DNA - The amazing information storage capacity of DNA - Getting the information in the genome - Getting the gene expression machinery to make proteins - Origin of the 37 gene codes: Did they evolve?
AL: Well, we have the demonstration by crystallography and this comes from the work of Lauren Williams and his friends, my colleagues at Georgia Tech, that if you look at the catalytic side of the large subunit of a ribosome, you don't have any proteins in the actual place where the peptide bond is being synthesized. Reply: The Ribosomal Peptidyl Transferase Center: Structure, Function, Evolution, Inhibition https://geneticacomportamento.ufsc.br/files/2013/08/Polacek05-Ribozima-peptidil-transferase.pdf The distinctive features of the modern ribosome are its mammoth size and enormous structural complexity. The molecular weight of the ribosome exceeds 2.5 million daltons and the particle comprises at least three large rRNA molecules and more than 50 different ribosomal proteins. It is unimaginable that the ribosome, which contains rRNAs of thousands of nucleotides in length, evolved in a single evolutionary step.
Peptide Bond Formation Mechanism Catalyzed by Ribosome https://sci-hub.st/https://pubs.rsc.org/en/content/articlelanding/2015/ra/c5ra02767e#!divAbstract By using an atomic mutagenesis approach to investigate all the 23S rRNA residues that compose the inner core of the peptidyltransferasecenter, we identified a single functional group with crucial importance for peptide bond catalysis— namely, theribose 20'-OH at A2451. This ribose 20 group needs to maintain hydrogen donor characteristics in order to promote effective amide bond formation.
Evidently, the positioning of all substrates, transition states, and ribosomal residues contributing to the concerted redistribution of charges must be tightly controlled to achieve efficient transpeptidation compatible with the observed in vivo rates of amino acid polymerization of about 20 s–1.
My comment:A precise, minutely orchestrated arrangement of just two main players, the interaction of ribose 2'-OH at position A2451 , and the 2’ hydroxyl of the P site substrate A76 are pivotal in orienting substrates in the active site for optimal catalysis, and play a key role in polypeptide bond formation. The ribosome promotes the reaction of the amino acid condensation by properly orienting the reaction substrates. Key in the reaction is the presence of a proton shuttling group. The observed 100-fold reduction in the reaction rate by mutation of P-site A76 20-OH group is indication of this group's activity during the peptidyl transfer reaction. There is no way, that such precision could have emerged by unguided prebiotic non-intelligent mechanisms. That is not an argument from ignorance or incredulity, but the fact that randomness has an extreme limit, basically neglectable, to bring forward such a highly orchestrated, precise, engineered, coordinated, and controlled process.
In the upper part of the tunnel, results suggest that A2062 and A2451 can communicate in both directions for translation stalling, mostly through dynamically coupled C2063, C2064, and A2450.
My comment: This is truly awe-inspiring. The functional group A2451, which is not only of crucial importance as described above for peptyde bond catalysis, but when the translation process is stalled, it signals to a dynamically coupled group in the exit tunnel of the product, the polypeptide chain: " we have a problem here",
AL: If you want to have RNA, you know that you need ribonucleotides, the ribonucleotides are synthesized here , but is essentially the same pathway, biochemical pathway, metabolic pathway, in all living entities that we have studied so far. Reply: True, but how did these extremely sophisticated and regulated pathways emerge prebiotically?
Nucleotides Folate is necessary for the production and maintenance of new cells , for DNA synthesis and RNA synthesis through methylation . The synthesis of NADPH requires six enzymes. 5Six proteins are required in the folate pathway. 4
RNA Nucleotides are building blocks for DNA and RNA. Three Pyrimidines and Two Purines Are Commonly Found in Cells. The pyrimidine synthesis pathway requires six regulated steps, seven enzymes, and energy in the form of ATP. The starting material for purine biosynthesis is Ribose 5-phosphate, a product of the highly complex pentose phosphate pathway, which uses 12 enzymes. 1 De novo purine synthesis pathway requires ten regulated steps, eleven enzymes, and energy in the form of ATP.
DNA The replacement of RNA as the repository of genetic information by its more stable cousin, DNA, provides a more reliable way of transmitting information. DNA uses thymine (T) as one of its four informational bases, whereas RNA uses uracil (U). At the C2' position of ribose, an oxygen atom is removed. The remarkable enzymes that do this are named Ribonucleotide reductases (RNR). The iron-dependent enzyme is essential for DNA synthesis, and most essential enzymes of life 32 , and it has one of the most sophisticated allosteric regulations known today. 50 The thymine-uracil exchange constitutes one of the major chemical differences between DNA and RNA. Before being incorporated into the chromosomes, this essential modification takes place. Uracil bases in RNA are transformed into thymine bases in DNA. The synthesis of thymine requires seven enzymes. De novo biosynthesis of thymine is an intricate and energetically expensive process. All in all, not considering the metabolic pathways and enzymes required to make the precursors to start RNA and DNA synthesis requires at least 26 enzymes.
1. On the one side, we have the putative prebiotic soup with the random chaotic floating around of the basic building blocks of life, and on the other side, the first living self-replicating cell ( LUCA ), a supposed fully operational minimal self-replicating cell, using the highly specific and sophisticated molecular milieu with a large team of enzymes which catalyze the reactions to produce the four basic building blocks of life in a cooperative manner, and furthermore, able to maintain intracellular homeostasis, reproduce, obtaining energy and converting it into a usable form, getting rid of toxic waste, protecting itself from dangers of the environment, doing the cellular repair, and communicate. 2. The science paper: Structural analyses of a hypothetical minimal metabolism proposes a minimal number of 50 enzymatic steps catalyzed by the associated encoded proteins. They don't, however, include the steps to synthesize the 20 amino acids required in life. Including those, the minimal metabolome would consist of 221 enzymes & proteins. A large number of molecular machines, co-factors, scaffold proteins, and chaperones are not included, required to build this highly sophisticated chemical factory. 3. There simply no feasible viable prebiotic route to go from a random prebiotic soup to this minimal proteome to kick-start metabolism by unguided means. This is not a conclusion by ignorance & incredulity, but it is reasonable to be skeptic, that this irreducibly complex biological system, entire factory complexes composed of myriads of interconnected highly optimized production lines, full of computers and robots could emerge naturally defying known and reasonable principles of the limited range of random unguided events and physical necessity. Comparing the two competing hypotheses, chance vs intelligent design, the second is simply by far the more case-adequate & reasonable explanation.
AL: If we want to have DNA, we need deoxyribonucleotides. And in absolutely all them entities, if you want to have deoxyribonucleotides, biochemistry needs to reduce very rapidly needs to reduce ribonucleotides to form deoxyribonucleotides. So this is a very strong biochemical arguments to assume that indeed RNA or at the very least ribonucleotides can vary to deoxyribonucleotides. Reply:
RNR enzymes are required to make DNA. DNA is however required to make RNR enzymes. What came first ?? We can conclude with high certainty that this enzyme buries any RNA world fantasies and any possibility of transition from RNA to DNA world scenarios.
AL: "Today's biosphere is DNA based and the only known RNA lifeforms are RNA viruses." And he puts his life on between quotation marks which I think is a very fair description of the issue of whether they are alive or not. These depend on DNA host cells for their existence. Reply: What came first : Viruses, or life?