The engineering of ribose enzymes does not mimic unguided chemical evolution.

The engineering of ribose enzymes does not mimic unguided chemical evolution. *Note: This article is from the book (Signature in the Cell: DNA and Intelligent Design Guides) for more please check out the book. Because of the difficulties of the RNA world hypothesis and the limited number of enzymatic functions that can be accomplished by naturally occurring ribosomal enzymes, a new laboratory industry has sprung up in molecular biology, as scientists championing the idea of the RNA world sought to design new RNA molecules with functions we had not seen before, thus hoping not only to increase their knowledge of RNA chemistry, but also to demonstrate the possibility of the RNA world hypothesis, and even the possibility of creating some sort of artificial life. Typically, these repository enzyme engineering experiments use one of two methods: the "sense design" method or the "directed evolution" method; in both cases, the biologists seek to generate more effective copies of new repository enzymes or ribosomal enzymes that are able to accomplish some other protein functions. In directed evolution (or "nonsensical design"), scientists try to simulate a form of prebiotic natural selection to produce ribosomal enzymes with improved functional capabilities, sifting through groups of RNA molecules using chemical traps to isolate molecules that accomplish certain functions, and after selecting these molecules from the group, generating various copies of these molecules. By random modification (mutation) of a part of the sequence of the original molecule, they then select the most functional molecules in this new group and repeat the process several times until it produces a measurable increase in the desired function. Most of the engineering of ribosomal enzymes has been done on ligases, which are ribosomes that can bind two RNA sequences (oligomers) together by forming a single bond (biester phosphorylation) between them, and ligase engineers want to prove that these ligases can also be converted into real polymerases or "ribloids", but these polymers will not bind only the nucleotide bases. Polymers are the holy grail and lost power of reboise enzyme engineering. According to the RNA world hypothesis, once a self-replicating polymerase is created by a template, it will make natural selection a factor in post-life chemical evolution, and since the ligase accomplishes one and only one of the many functions that real polymerase accomplishes, RNA world theorists have speculated that the ligase is the precursor molecules from which the polymers originated. No one has yet successfully engineered RNA-based polymerases based on fully functional RNAs, both from Ligaz and elsewhere.41 But engineers of ribosome enzymes have used directed evolution to improve the function of some common types of ligazes, and as we have already noted, they have also produced a molecule that can replicate a small fraction of itself. However, these claims have a clear disadvantage: engineers of ribosomal enzymes tend to overlook the role of their intelligence in improving the functional capabilities of the RNA catalysts they have produced, as the way engineers have used their intelligence to aid directed evolution has no equivalent in prebiotic world conditions – at least in a world where only non-directional processes have driven chemical evolution forward – although these are the same conditions that ribosomal enzyme experiments are supposed to simulate. Proponents of the transcriptional world imagine the evolution of ligases through a non-directed process, starting with free bases, or using ligase-enhanced polymerases that can multiply themselves, and then creating the conditions for the beginning of natural selection, in other words; these experiments try to simulate a transition that occurs, according to the theory of the RNA world, before natural selection has even begun, but until they have improved the function of the ligase molecules, they have actually simulated what natural selection does. Improvement in desired function. Shostak and his colleagues did not tell us, surely they cannot say that natural selection played this role, because the process of natural selection depends on the prior creation of the self-replicating molecule that Shostak and his colleagues are working to design, but instead Shostak and his colleagues have practiced a role that nature cannot before the creation of a self-replicating system, or at least a self-replicating molecule. Shostak and his colleagues worked multiples, generating a large amount of different sequences, choosing sequences that would remain to undergo another round of directed evolution, and even choosing them based on a future insight that neither natural selection nor any unintelligent or undirected process (by itself),43 the features of the RNA molecules that Shostak and his colleagues isolated and selected do not themselves confer any functional advantage over the precellular molecule in the world. Of course, ligase enzymes perform functions within contemporary cells that give a selective advantage to the cells they contain, but before the creation of the first self-replicating protocell, ligase ribosomes had no functional advantage over other RNA molecules, so at this stage of chemical development there was no self-replicating system to give them any benefit. The ability to bind nucleotide chains is essential (at its best), but it is not sufficient to perform the function of polymerase or ribalcase, and in the absence of a molecule (or molecular system, which is more likely) with all the features required for self-replication, nature will not prefer any RNA molecule to other molecules; natural selection never plays a role other than that of functionally useful ones, and in self-replicating systems only possible. Thus, even if ribo-enzyme experiments significantly improve RNA-catalyst capabilities, this does not mean that they have demonstrated the possibility of unguided chemical evolution. Since the experiments in engineering ribo-enzymes have a clearer role for intelligence as they use sane design (as opposed to direct evolution), they still reflect the same problem. 40. Szostak, Bartel, and Luisi, “Synthesizing Life.” 41. Szostak, Bartel, and Luisi, “Synthesizing Life,” 388; Wolf and Koonin, “On the Origin of the Translation System.” 42. Eckland et al. claimed that effective ribosomes are more common in RNA sequence assemblies than previously thought ("Structurally Complex and Highly Active RNA Ligases", especially in 364). The area of sequences (the total number of possible nucleotide combinations) corresponding to 220-base RNA molecules. Given that they were able to isolate the ribosome of the ligas by searching for a small fraction of the entire area (about 1.4 x 1015 separate sequences), this meant that the entire area would contain a huge number of comparable ligas. But in order for such a simple function to require a single sequence in a trillion, it raises serious questions about the scarcity of more complex functions. As noted, for example, the engineering of ribosomal enzymes has not yet produced a single ribozyme capable of performing true polymerase activity. 43. As Wolf and Konin note: "Because evolution has no foresight, no system can evolve with the expectation that it will become useful once the required level of complexity is reached." Wolf, Yuri I., and Eugene V. Koonin. “On the Origin of the Translation System and the Genetic Code in the RNA World by Means of Natural Selection, Exaptation, and Subfunctionalization.” Biology Direct 2 (2007): 1–25. - Dr. Steven Meyer. — Source: Brahin Center website - Published on 2018-10-12 (archived at the Internet Archive) https://braheen.com/articles/evolution-design/هندسة-الإنزيمات-الريبوزية-لا-تحاكي-التطور-الكيميائي-غير-الموجه