Defending the Christian Worlview, Creationism, and Intelligent Design
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Defending the Christian Worlview, Creationism, and Intelligent Design

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Defending the Christian Worlview, Creationism, and Intelligent Design » Molecular biology of the cell » Main topics on Proteins and Protein synthesis

Main topics on Proteins and Protein synthesis

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Proteins and Protein synthesis

Proteins are structures of complex semantophoretic macromolecules that carry genetic information.

Researchers are debating whether function or structure first appeared in primitive peptides September 23, 2013
Proteins Red protein structure, generictraverse the width and breadth of cells to carry signals and cargo from one end to another, package and replicate DNA, build scaffolds to give cells their shapes, break down and take up nutrients, and so much more. But how often do we stop to ask: How did these diverse and sophisticated molecular machines come to be? Despite proteins' profound impact on life, their origin is not well understood. What caused a string of amino acids to start doing something? Or are strings of amino acids inherently programmed to do things? These are questions with which researchers in the protein-origin field have been grappling.

Researchers have a better grasp of the processes of selection and evolution once a function appears in a peptide. “Once you have identified an enzyme that has some weak, promiscuous activity for your target reaction, it’s fairly clear that, if you have mutations at random, you can select and improve this activity by several orders of magnitude,” says Dan Tawfik at the Weizmann Institute in Israel. “What we lack is a hypothesis for the earlier stages, where you don’t have this spectrum of enzymatic activities, active sites and folds from which selection can identify starting points. Evolution has this catch-22: Nothing evolves unless it already exists.

François Jacob: Evolution and Tinkering Jun. 10, 1977
A sequence of a thousand nucleotides codes for a medium-sized protein. The probability that a functional protein would appear de novo by random association of amino acids is practically zero. In organisms as complex and integrated as those that were already living a long time ago, creation of entirely new nucleotide sequences could not be of any importance in the production of new information.

A. G. CAIRNS-SMITH Seven clues to the origin of life, page 30:
Nothing evolves that is not somehow tied into the successions of messages. Nor could the precision of manufacture have been much less if it was enzymes that were needed right away. Darwin persuades us that the seemingly purposeful construction of living things can very often, and perhaps always, be attributed to the operation of natural selection. A clumsy enzyme is a good bit worse than useless if it is continually transforming molecules the wrong way, or transforming the wrong molecules. More and more molecules would be produced that had been wrongly put together, and these would include components for RNA adaptors, ribosomes, etc. - leading to further badly made enzymes and a rapid slide into chaos. Nor does it take much for an enzyme to become incompetent. The whole technique of operation requires that the protein message folds up in a way that depends on the sequence of amino acid units. Even having only one mistake, one wrongly inserted amino acid, can wreck any chance of a correct folding; and more than a few mistakes are almost bound to. It is not just the sheer size of even the smallest libraries; it is not just that nucleotide units are rather complex in themselves, and rather difficult to join together (because Nature is on the side of keeping them apart); it is not just the need for enzymes, here, there and everywhere; it is not just that enzymes are of little use unless they have been made properly; it is not just that ribosomes are so very sophisticated - and look as though they would have to be to do their job; it is not just such questions relating to the particular kind of life that we are familiar with. There seems also to be a more fundamental difficulty. Any conceivable kind of organism would have to contain messages of some sort and
equipment for reading and reprinting the messages: any conceivable organism would thus seem to have to be packed with machinery and as such need a miracle (or something) for the first of its kind to have appeared. That's the problem.

How Did Protein Synthesis Evolve?
The molecular processes underlying protein synthesis in present-day cells seem inextricably complex. Although we understand most of them, they do not make conceptual sense in the way that DNA transcription, DNA repair, and DNA replication do. It is especially difficult to imagine how protein synthesis evolved because it is now performed by a complex interlocking system of protein and RNA molecules; obviously the proteins could not have existed until an early version of the translation apparatus was already in place. As attractive as the RNA world idea is for envisioning early life, it does not explain how the modern-day system of protein synthesis arose.
Molecular biology of the cell, 6th ed. pg. 365

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.

Estimating 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.

Proteins: how they provide striking evidence of design

Proteins are evidence of intelligent design par excellence. Instructional/specified complex information is required to get the right amino acid sequence which is essential to get functionality in a vast sequence space ( amongst trillions os possible sequences, rare are the ones that provide function ), and every protein is irreducibly complex in the sense, that a minimal number of amino acids are required for each protein to get function. This constitutes an insurmountable hurdle for the origin of life scenarios based on naturalistic hypotheses since unguided random events are too unspecific to get functional sequences in a viable timespan. Another true smack-down is the fact that single proteins or enzymes by themselves confer no advantage of survival at all, and have by their own no function. There is no reason why random RNA strands would become self-replicating. And even IF that were the case, so what? There would be no utility for them unless at least 50 different precisely arranged and correctly interlinked enzymes and proteins, each with its specific function, would interlink in a complex, just right metabolic network, and be encapsulated in a complex membrane with gates and pores, and in a precisely finely tuned and balanced homeostatic ambiance. Energy production and supply to each protein would also have to be fully set up right from the start...... hard to swallow. But if your wish of naturalism to be true is strong enough, just shut your reason up, and believe this. Blindly.

It is not surprising that various studies on evolving proteins have failed to show a viable mechanism. One study concluded that 10^63 attempts would be required to evolve a relatively short protein. And another study concluded that 10^70 attempts would be required. So something like 10^70 attempts are required yet proponents of evolution estimate that only up to a probability of 10^43 attempts would be in the realm of possible. In other words, there is a shortfall of 27 orders of magnitude. But it gets worse.

The impossible task to synthesize proteins on a prebiotic earth without external direction

Eliminative inductions argue for the truth of a proposition by arguing that competitors to that proposition are false. There was no sufficient nitrogen fixation on a prebiotic earth. The sufficiency of ammonia has also been brought into question. The source of sorting out of right-handed DNA and left-handed amino acids on a prebiotic earth is unsolved for decades. A recent science paper reported that the set of amino acids selected, being used in life, appears to be near ideal. Why the particular 20 amino acids were selected to be encoded by the Genetic Code remains a puzzle. This is nothing short than astounding. Why were they selected amongst over 500 different ones known? Amino acid synthesis requires essential regulation. How could that have been achieved without evolution? Regulation requires a regulator - or - intelligence.

Lifeless matter has no teleological goal to regulate things. How the amino acids would and could have been bonded together in the correct manner without the Ribosome is another unsolved question. The probability is far higher that polymers would disintegrate, rather than the opposite. How could natural processes have foresight, which seems to be absolutely required, to "know" which amino acid sequences would provoke which forces, and how they would fold the protein structure to get functional for specific purposes within the cell? Let's consider, that in order to have a minimal functional living cell, at least 561 proteins and protein complexes would have to be fully setup, working, and interacting together to confer a functional whole with all life-essential functions.

Many proteins require " help " proteins to fold correctly. Also, some which were essential for life to begin. How should and could natural nonintelligent mechanisms forsee the necessity of chaperones in order to get a specific goal and result, that is functional proteins to make living organisms? Nonliving matter has no natural " drive " or purpose or goal to become living. The make of proteins to create life, however, is a multistep process of many parallel acting complex metabolic pathways and production-line like processes to make proteins and other life essential products like lipids, carbohydrates etc. The right folding of proteins is just one of several other essential processes in order to get a functional protein. But a functional protein by its own has no function unless correctly embedded through the right order of assembly at the right place.

Last not least, this is probably one of the most screaming problems: For biological cells 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, which makes its origin an irreducible  catch22 problem.

Medical Research Council Unit for the Study of Molecular Biology, Cavendish Laboratory, Cambridge

The nature of protein synthesis:
The basic dilemma of protein synthesis has been realized by many people, but it has been particularly aptly expressed by Dr A. L. Dounce (1956); My interest in templates, and the conviction of their necessity, originated from a question asked me on my PhD oral examination by Professor J. B. Sumner. He enquired how I thought proteins might be synthesized. I gave what seemed the obvious answer, namely, that enzymes must be responsible. Professor Sumner then asked me the chemical nature of enzymes, and when I answered .that enzymes were proteins or contained proteins as essential components, he asked whether these enzyme proteins were synthesized by other enzymes and so on ad Infinitum. The dilemma remained in my mind, causing me to look for possible solutions that would be acceptable, at least from the standpoint of logic. The dilemma, of course, involves the specificity of the protein molecule, which doubtless depends to a considerable degree on the sequence of amino acids in the peptide chains of the protein. The problem is to find a reasonably simple mechanism that could account for specific sequences without demanding the presence of an ever-increasing number of new specific enzymes for the synthesis of each new protein molecule. It is thus clear that the synthesis of proteins must be radically different from the synthesis of polysaccharides, lipids, co-enzymes and other small molecules; that it must be relatively simple, and to a considerable extent uniform throughout Nature; that it must be highly specific, making few mistakes; and that in all probability it must be controlled at not too many removes by the genetic material of the organism.

a kinases is an enzyme that catalyzes the transfer of phosphate groups from high-energy, phosphate-donating molecules to specific substrates.
Isomerases are a general class of enzymes that convert a molecule from one isomer to another.
dehydrogenase (also called DH or DHase in the literature) is an enzyme belonging to the group of oxidoreductases that oxidizes a substrate by reducing an electron acceptor, usually NAD+/NADP+ or a flavin coenzyme such as FAD or FMN.

The estimated number of sequences capable of adopting the h repressor fold is still an exceedingly small fraction, about one in 10^63 of the total number of possible 92-residue sequences.

The interdependent and irreducible structures required to make proteins

Peptide bonding of amino acids to form proteins and its origins

Forces Stabilizing Proteins - essential for their correct folding

Proteins: how they provide striking evidence of design

Biosynthesis of Iron-sulfur clusters, basic building blocks for life

Titin the largest proteins known and titin-telethonin complex - the strongest protein bond found so far in nature

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