Intelligent Design, the best explanation of Origins
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Intelligent Design, the best explanation of Origins

This is my personal virtual library, where i collect information, which leads in my view to Intelligent Design as the best explanation of the origin of the physical Universe, life, and biodiversity


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226My articles - Page 10 Empty Re: My articles on Fri May 29, 2020 7:11 am

Otangelo


Admin
Biochemical fine-tuning - essential for life

https://reasonandscience.catsboard.com/t2591-biochemical-fine-tuning-essential-for-life

The fact that abiogenesis is not possible becomes evident and clear to anyone considering this: The basic building blocks that makeup life are four: nucleotides, amino acids, phospholipids, and carbohydrates. To illustrate my point, i will mention just nucleotides:

Nucleotides are composed of three distinctive chemical sub-units: a five-carbon sugar molecule, a nitrogenous base, and one phosphate group.

Ribose is sugar with five primes. Nucleobases must be always attached at the one prime end with glycosidic bonds,  and phosphate groups at the 5 prime end, and joining the next nucleotide monomer for polymerization at the  3 prime positions.

There NO prebiotic natural selection that constraints the attachment of the phosphate group at these two positions, and worse, in a repetitive manner. It can be anywhere on the five primes.

The same problem is in regards to the correct position of nucleobases at the one prime position. Not only is there no prebiotic glycosidic bond formation process known, but there is no natural selection to attach the base at the one prime position, in a repetitive manner.

Nucleobases, pyrimidine, and purines require to have planar, flat shapes, in order to be able to bond together. The nitrogenous bases form hydrogen bonds between opposing DNA strands to form the rungs of the "twisted ladder" or double helix of DNA. If they were not complementary in the right way, they would not form the DNA ladder. But there is natural selection either to produce the right forms.

AmazingWatson–Crick base-pairing
The existence of Watson–Crick base-pairing in DNA and RNA is crucially dependent on the position of the chemical equilibria between tautomeric forms of the nucleobases.1 These equilibria in both purines and pyrimidines lie sharply on the side of amide- and imide-forms containing the (exocyclic) oxygen atoms in the form of carbonyl groups (C=O) and (exocyclic) nitrogen in the form of amino groups (NH2). The positions of these equilibria in a given environment are an intrinsic property of these molecules, determined by their Physico-chemical parameters (and thus, ultimately, by the fundamental physical constants of this universe). The chemist masters the Herculean task of grasping and classifying the boundless diversity of the constitution of organic molecules by using the concept of the “chemical bond.” He pragmatically deals with the differences in the thermodynamic stability of molecules by using individual energy parameters, which he empirically assigns to the various types of bonds in such a way that he can simply add up the number and kind of bonds present in the chemical formula of a molecule and use their associated average bond energies to estimate the relative energy content of essentially any given organic molecule.

Now comes the striking interpretation of the Darwinism-inclined and indoctrinated mind :

Whatever biological phenomena appear fine-tuned can be interpreted in principle as the result of life having finetuned itself to the properties of matter through natural selection. Indeed, to interpret in this way what we observe in the living world is mainstream thinking within contemporary biology and biological chemistry.

Sometimes it strikes me how un-imaginative these folks are. They cannot imagine anything else besides NATURAL SELECTION. So the hero on the block strikes again. The multi-versatile mechanism propagated by Darwin explains and solves practically any issue and arising question of origins. Can't explain a phenomenon in question? NS did it.....  huh...

This alone is a real KILLER for abiogenesis.  If scientists would consider it, they would move on to other scientific fields, and forget about attempting to solve the riddle of the origin of life by natural unguided means.  Its, simply stated, IMPOSSIBLE !!

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227My articles - Page 10 Empty Re: My articles on Sat Jun 13, 2020 10:38 am

Otangelo


Admin
mRNA stands for messengerRNA.

In my view, it should be correctly named messageRNA. It is a message carrier. The messenger is God, who encoded the message, the blueprint, the instructional complex information in DNA, where it is transcribed to mRNA, and translated in the Ribosome into proteins.

Not many have a grasp of how many molecular machines are involved in the cell to make RNA. Let me give an idea of the complexity of just one of them.

Aspartate Carbamoyltransferase is the second enzyme in the production line - like process to make Pyrimidines, one of the two types of nucleobases to make RNA and DNA:

Enzymes used in the process:

1. Carbamoyl phosphate synthase II
2. Aspartate carbamoyltransferase
3. Dihydroorotase
4. Dihydro Orotate Dehydrogenase
5. Orotate Phosphoribosyl transferase
6. Orotidine 5'-phosphate decarboxylase
7. Nucleoside-phosphate kinase & Nucleoside-diphosphate kinase

Consider, that in regards to its origin, NONE of all these molecular machines can be explained by Darwinian evolution, because evolution depends on DNA replication. So either this machinery emerged prebiotically by a lucky accident, spontaneously through self-organization by unguided natural events in an orderly manner without external direction, chemical non-biological, purely physicodynamic processes and reactions, or through the direct intervention and creative force of an intelligent agency, a powerful creator.

https://reasonandscience.catsboard.com/t2028-the-dna-double-helix-evidence-of-design#3426

From: David Goodsell, Our Molecular Nature, page 26

Dozens of enzymes are needed to make the DNA bases cytosine and thymine from their component atoms. The second step is performed by aspartate carbamoyltransferase. In bacteria, this enzyme controls the entire pathway. (In human cells, the regulation is more complex, involving the interaction of several of the enzymes in the pathway.) The enzyme is composed of six large catalytic subunits and six smaller regulatory subunits . The active site of the enzyme is located where two individual catalytic subunits touch, so the position of the two subunits relative to one another is critical. Take just a moment to ponder the immensity of this enzyme. The entire complex is composed of over 40,000 atoms, each of which plays a vital role. The handful of atoms that actually perform the chemical reaction are the central players. But they are not the only important atoms within the enzyme--every atom plays a supporting pan. The atoms lining the surfaces between subunits are chosen to complement one another exactly, to orchestrate the shifting regulatory motions. The atoms covering the surface are carefully picked to interact optimally with water, ensuring that the enzyme doesn't form a pasty aggregate, but remains an individual, floating factory. And the thousands of interior atoms are chosen to fit like a jigsaw puzzle, interlocking into a sturdy framework. Aspartate carbamoyltransferase is fully as complex as any fine automobile in our familiar world.

to make purines, it is even more complex, and more enzymes are required:

The enzymes of de novo purine synthesis

Phosphoribosyl-pyrophosphate synthetase (Prs)

1. Ribose-phosphate diphosphokinase
2. amidophosphoribosyl transferase
3. Phosphoribosylglycinamide formyltransferase ( GAR )
4. Phosphoribosylaminoimidazole carboxylase
5. Dihydrofolate reductase
6. AIR synthetase
7. AIR carboxylase
8. SAICAR synthetase
9. adenylosuccinase (adenylosuccinate lyase)
10. AICAR transformylase
11. IMP cyclohydrolase

And all this technology is required only to make the bases, not the assembly to have RNA. To go from RNA to DNA is requires even more ultrasophisticated molecular machines, like Ribonucleotide Reductase, which is formidably complex.

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228My articles - Page 10 Empty Re: My articles on Mon Jul 06, 2020 5:58 am

Otangelo


Admin
According to an estimate made by engineers at Washington University, there are around 10^14 atoms in a typical human cell. Another way of looking at it is that this is 100,000,000,000,000 or 100 trillion atoms. Interestingly, the number of cells in the human body is estimated to be about the same as the number of atoms in a human cell. 1

A human cell hosts about 2 billion proteins. 2

Let's give a closer look to just one protein. Aspartate Carbamoyltransferase

The active site of the enzyme is located where two individual catalytic subunits touch, so the position of the two subunits relative to one another is critical. Take just a moment to ponder the immensity of this enzyme. The entire complex is composed of over 40,000 atoms, each of which plays a vital role. The handful of atoms that actually perform the chemical reaction are the central players. But they are not the only important atoms within the enzyme--every atom plays a supporting pan. The atoms lining the surfaces between subunits are chosen to complement one another exactly, to orchestrate the shifting regulatory motions. The atoms covering the surface are carefully picked to interact optimally with water, ensuring that the enzyme doesn't form a pasty aggregate, but remains an individual, floating factory.

Fine-tuning in biochemistry is represented by the strength of the chemical bonds that makes the universal genetic code possible. Neither transcription nor translation of the messages encoded in RNA and DNA would be possible if the strength of the bonds had different values. Hence, life, as we understand it today, would not have arisen. 3

As it happens, the average bond energy of a carbon–oxygen double bond is about 30 kcal per mol higher than that of a carbon–carbon or carbon–nitrogen double bond. If the difference between the average bond energy of a carbon–oxygen double bond and that of a carbon–carbon and carbon–nitrogen double bond were smaller by a few kcal per mol, then the nucleobases guanine, cytosine, and thymine would exist as “enols” and not as “ketones,” and Watson–Crick base-pairing would not exist – nor would the kind of life we know.

My comment: That means, the atom composition of the DNA nucleobases most be of the right atoms to guarantee the right hydrogen bond forces that permit Watson-Crick base-pairing.



1. https://www.thoughtco.com/how-many-atoms-in-human-cell-603882
2. http://book.bionumbers.org/how-many-proteins-are-in-a-cell/
3. Barrow, FITNESS OF THE COSMOS FOR LIFE,  Biochemistry and Fine-Tuning, page 154

4. https://sci-hub.tw/https://www.sciencedirect.com/science/article/abs/pii/S037015731630028X

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229My articles - Page 10 Empty Imagine... on Thu Jul 09, 2020 1:20 pm

Otangelo


Admin
Imagine...

you were invited to go to a martial art fight and had the opportunity to bet on the fight, and if you won, become one of the wealthiest persons imaginable. Gaining more money than the ten richest men on earth together. Richer than the Rothschilds. You had two options to chose, two fighters, being:

Option one: The best, most capable, best trained, best-equipped fight warrior ever seen:
fully armored extraordinarily life-long trained professional warrior prepared for any fight,  applying advanced and developed fighting skills and tactics, highly capable, planning how to fight by studying and understanding his opponent, thoughtful, knowledgeable, experienced, using foreplanning and judgment of how to perform the fight, reasons and thinks how to apply complex fight techniques, observing and perceiving his surrounding, and adapting and adjusting effectively to the conditions of the fight, calculating, applying stored information of previous experience.

Option two:
you have a warrior, which just appears like a warrior, but is, in reality, a mindless, brainless, blind, earless lifeless bot, with no sensory perception at all, just standing there like a show doll in the vitrine.

Any sane person would obviously bet on option one, the capable warrior, which, in an instant, would shred the bot into peace and not leaving other than snippets of peace on the ground.

Theists are those that opt to choose in a debate the capable warrior. Atheists, option two, the mindless bot. It's OBVIOUS when armored with good arms, theists win an intellectual fight. The arms are knowledge in philosophy, theology, and science.

God is comparable with the capable warrior.

An intelligent designer can create:

- an object in nature very similar to human-made things
- something made based on mathematical principles
- systems and networks functioning based on logic gates
- something purposefully made for specific goals
- specified complexity, the instructional blueprint or a codified message  
- irreducible complex and interdependent systems or artifacts composed of several interlocked, well-matched parts contributing to a higher end of a complex system that would be useful only in the completion of that much larger system.
- order or orderly patterns
- hierarchically arranged systems of parts
- intelligence can create artifacts which use might be employed in different systems ( a wheel is used in cars and airplanes )
- Fine-tuning

No agent at all, that is:

- fortuitous accidents
- spontaneous self-organization
- unguided stochastic coincidence
- events without external direction
- reactions influenced by environmental parameters

can not.

An Intelligent Designer can climb mount unsurmountable, that is:

- trigger the Big bang, and create a finely tuned and adjusted universe
- invent mathematical laws which enforce how matter behaves  
- finely tune on a razor's edge the conditions to make stars, essential for life, which is a chance of one in 10^209 ( a vanishingly small number )  Chance practically zero.
- create the complex building blocks of life
- select the four nucleobases, and the 20 amino acids, amongst hundreds extant on the early earth.
- create the extremely complex molecular machinery, and chemical factory, producing the basic building blocks of life.
- create energy in the form of ATP
- codified instructional complex information, stored in a minimal genome of 500 thousand nucleotides.
- set up a minimal proteome to have a functional cell with 438 proteins. Chance to get those randomly is 1 in 10^350.000
- create cells that are interdependent and irreducible complex ( a minimal genome, proteome, and metabolome size are required to give life a first go ).
- create millions of different lifeforms, different body architectures, and forms, based on preprogrammed instructional complex INFORMATION encoded in various genetic and epigenetic languages and communication by various signaling codes through various signaling networks. That brings us to the origin of an intelligent designer.
- create conscience and personality
- create and enforce in our hearts objective moral values
- create humans that seek for meaning and truth

No agent, can with high certainty, most probably, not.

It is obvious, that the theist is on the winning side. And, provided with a good education, will win every debate with atheists in the sense of most likely being on the side of the worldview which is true. And his winning price cannot be bought with all wealth existing on earth: Eternal life in the presence of the triune loving, just, graceful, forgiving, good, immensely powerful creator.

What is your choice? In which team do you want to play?


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230My articles - Page 10 Empty Re: My articles on Fri Jul 10, 2020 7:06 am

Otangelo


Admin
Lies are successful when they are hidden. We don't believe lies when they are explicitly untrue, and when it is easy to recognize, that the claim does not correspond to reality.

When we hear the word select, and the question is, what the agency is, that does select, immediately we relate it to intelligence.

Select means to have a choice, and willingly to select either between a few, or a multitude of options. But it is always a conscient process, requiring a mind.

In nature, the complexity of the living depends on the extreme complex organization of matter into a form that permits life.

Reproduction, the means of obtaining energy in whatever form that may have been, the means of converting that energy source to a useable form, the means of ridding itself of toxic waste, the means of protecting itself from environmental dangers ex, radiation, temperature fluctuations, acid/base conditions, means of cellular repair of all of these mechanisms. The means of intracellular communication between all its parts the prior knowledge that it would need all these components and the ability of ALL of these to function fully and simultaneously from day one because malfunctions of, or incomplete versions or not fully "evolved" parts would have lead to immediate or almost immediate death.

Either cells are able, all at once, to perform these actions, or to survive is not possible. All stepwise "down-up" proposals to get to the complexity needed to perform all these actions by natural means have failed. But the cop-out is: Science is working on it.

Proponents of evolution have been successful to remove the correlation of selection to intelligent action, and attribute it to nature, a mindless, unguided natural process. Natural selection is echoed to be the hero on the block, responsible for all biodiversity on earth. A rather simple process is hailed to be responsible for the human brain, the most complex structure known in the universe, consisting of hundreds of billions of neurons, each with tens of thousands of dendritic branches, forming a web that generates and shares information with other neurons, of unimaginable complexity.

Many times, creationists have to hear the canard: " You don't know how evolution works ". Suddenly, every atheist average Joe has become an expert, and feels himself in the high position to arrogantly look down to creationists, and claim that creationists " don't know how evolution works ".  When I hear that phrase, I smile. I immediately think: This guy suffers from the Dunning Kruger effect, and ultracrepidarianism. Truth is, even experts do NOT KNOW how evolution supposedly works. It has been ever since and keeps being a metaphysical research program without hard evidence. A religious claim incorporated in the atheist's toolbox as the holy grail. Because evolution is true, we can get rid of God, its the all-encompassing explanation that replaces God. Why do you think God is not necessary? Oh !! We have evolved. I heard that over and over.  

The lie is buried deep down. One has to dig deep and understand biology. One has to understand what unguided mechanisms are capable of, and where the limits are. Atheists believe natural unguided events can do basically everything, given enough time.  And when taught at school, and endorsed by the scientific establishment, and when there is consensus, then the average Joe thinks there is enough ground to adhere to the claims and adopt them. Its, after all, published in peer-reviewed papers. Faith in science. Faith in men. That's enough to ridicule when others are skeptics or reach other conclusions.

Truth is, life, in order to be created, and on top of that, the biodiversity seen on earth depends on the input of information. Lots of it. Not just the selection of accidental mutations. But an initial injection of enormous amounts of information, and a storage mechanism, that is also generated through information input. And that information generates signals and instruction manuals. Which needs to be transmitted, and decoded, and that process generates the molecules, machines, production lines, factories, signaling networks, metabolic networks, etc seen in biology. It is a closed circle which had to start all at once from scratch.

Nature is incapable to select whatever is needed, to generate this complexity. Only intelligent minds, a super-intellect, could do such things. For that reason, creationism makes sense. Materialism does not.

Natural selection is a lie that was well hidden. But unmasked, we now know the truth. Most probably, God did it.

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231My articles - Page 10 Empty Re: My articles on Thu Jul 23, 2020 7:36 am

Otangelo


Admin
Electromagnetism & Morphogenesis, by evolution, or design?

1. One of the widely debated key questions in evolutionary biology is if traditional claims based on genetic mutations, natural selection, drift, and gene flow explain sufficiently the creation and maintenance of organismal form, complex biological systems, from cellular to body, guiding morphogenesis.

2. Recent groundbreaking scientific discoveries are demonstrating that one key issue, cell migration (galvanotropism, galvanotaxis or electrotaxis) is not due to change in allele frequencies in genes, but endogenous electric currents and fields, generated by molecules, program the formation of extracellular molecular gradients which play ai instructive role, guiding and generating cues of the migratory trajectory of cells to their end destination in the body during development. Complex pattern formation requires mechanisms to coordinate individual cell behavior towards the anatomical needs of the organism. Alongside the well-studied biochemical and genetic signals functions an important and powerful system of bioelectrical communication. All cells, not just excitable nerve, and muscle utilize ion channels and pumps to drive standing gradients of ion content and transmembrane resting potential. Bioelectrical properties are key determinants of cell migration, differentiation, and proliferation. Spatio-temporal gradients of transmembrane voltage potentials are instructive cues that encode positional information and organ identity, and thus regulates the creation and maintenance of large-scale shape. In a variety of model systems, it is now clear that bioelectric pre patterns function during embryonic development, organ regeneration, and cancer suppression."

3. Furthermore, the collective oscillations of calcium Ca2+ ions on the surface of cell membranes also contribute to generating endogenous electromagnetic fields and there is information encoded both in the amplitude modulation and in the frequency modulation of Ca2+ oscillations. Calcium (Ca2+) oscillations are ubiquitous signals present in all cells providing efficient means to transmit intracellular biological information. They regulate a wide spectrum of cellular processes, including fertilization, proliferation, differentiation, muscle contraction, learning, and cell death. Information encoded in Calcium (Ca2+) oscillations generate a huge spatial and temporal diversity of signals since a Ca2+ response can exhibit infinite patterns. Through an intricate concert of action between several Ca2+ transporters in the cell, the cytosolic Ca2+ concentration can start to oscillate, much like a radio signal. Specific information can thereby be efficiently encoded in the signal and transmitted through the cell without harming the cell itself. These endogenous electric fields generate three-dimensional coordination systems for embryo development. The genome is tightly linked to bioelectric signaling, via ion channel proteins that shape the gradients, downstream genes whose transcription is regulated by voltage, and transduction machinery that converts changes in bioelectric state to second-messenger cascades. The data clearly indicates that bioelectric signaling is an autonomous layer of control not reducible to a biochemical or genetic account of cell state.

4. Programming, the generation of instructions for complex pattern formation, coordination, communication, the encoding of information, orchestration of actions, the generation of informational radio signals, it's encoding, transmission, and decoding are all things exclusively done by intelligent minds with preset goals.

5. All those things are observed during morphogenesis and the development of complex organismal architecture. Therefore, the source of the biological development of complex multicellular organisms is best explained by intelligent design.

https://reasonandscience.catsboard.com/t2982-electromagnetism-morphogenesis

Image:
Structural evidence for electromagnetic resonance in plant morphogenesis
https://sci-hub.tw/https://www.sciencedirect.com/science/article/abs/pii/S0303264712000329

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232My articles - Page 10 Empty Gene expression, and self-replication on Tue Jul 28, 2020 10:42 am

Otangelo


Admin
Gene expression, and self-replication point to intelligent design

One of the two central processes in biological cells is gene expression and self-replication. They are irreducible. If one would be missing, no life and life perpetuation would be possible. 

Maintaining genomic integrity is essential for the cell. Genes are constantly monitored and scanned through electric pulses, which are sent in the chromosomes from one end to the other, and if lesions are detected, specific molecular machines fix the error. 1 The information stored in DNA has to be expressed to build the cell, and during transcription through RNA polymerase machines, and translation through the ribosome, several-error check, and repair mechanisms have to guarantee that the error rate is as low as one error in ten billion nucleotides 1. In the ribosome, the complex factory that makes proteins by translating the mRNA message to the amino acid alphabet alone, a staggering 11 error check and repair mechanisms are at play. That demonstrates, how important precision and a low error-rate are in the process.11   
In the next step, proteins are folded into their tertiary and quaternary structure. Since commonly they use metal co-factors that catalyze the enzymatic reactions, ( which are by themselves awe-inspiringly complex ) they have to be inserted with precision into the active site of the proteins.

Proteins, after the fold, are inserted in barrel-shaped proteins, chaperones 2, which correct any misfolding.  Then, another molecular machine, the indispensable signal recognition particle 3 tags the protein, prior to going to its final destination, and amongst other transport methods, kinesin and myosin cargo carriers which act like mini taxis 4 which are particularly fascinating, carry the protein cargo on microtubules, literal highways on nanoscale 5. Remarkably, these microtubules have a roadmap encoded in their structure, leading the taxis in the direction to the final destination where the proteins will be employed to do their job.

This is, of course, a very simplified description.  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 to make them, which makes its origin an irreducible  catch22 problem 10

In order for life to perpetuate, cells have to be capable to do what no known man-machine can do: Self replicate. Remarkably, the machinery in prokaryotic cells is different than in eukaryotes.7 ( That raises the question of how common ancestry of all life forms could be true 8  )  In order for the replication process to occur, a true armada of molecular machines come into play. In eukaryotes, up to 600 different proteins are required.  Amongst them helicase, one of the most fascinating and complex molecular machines known. 9 . It works with an astonishing velocity of 10000 rotations per minute !! DNA replication is also a process that is constantly monitored, error checked, and errors are repaired to maintain a tolerable mutation rate. Once, DNA is copied, the cell cycle and mitosis can begin. During the process, 16 cell cycle regulators are essential and irreducible. They monitor the entire process, and if one of these regulators are missing, no deal and the cell can not divide. 

Of course, all the nano-tech production lines and factories to make all this happen, including the error check and repair mechanisms, had to be in place right from the start, otherwise, no deal, and life as we know it, would never have taken off. 

I have not enough faith to believe, all this started by a freaky accident in a prebiotic soup. Do you ?!  

https://www.youtube.com/watch?v=vP8-5Bhd2ag&feature=emb_title

1. https://reasonandscience.catsboard.com/t2043-dna-and-rna-error-checking-and-repair-amazing-evidence-of-design#3498
2. https://reasonandscience.catsboard.com/t1437-chaperones
3. https://reasonandscience.catsboard.com/t2651-signal-recognition-particle-an-essential-protein-targeting-machine
4. https://reasonandscience.catsboard.com/t1448-kinesin-and-myosin-motor-proteins-amazing-cargo-carriers-in-the-cell
5. https://reasonandscience.catsboard.com/t2096-the-astonishing-language-written-on-microtubules-amazing-evidence-of-design
6. https://reasonandscience.catsboard.com/t1849-dna-replication-of-prokaryotes
7. https://reasonandscience.catsboard.com/t2233-dna-replication-of-eukaryotes
8. https://reasonandscience.catsboard.com/t2239-evolution-common-descent-the-tree-of-life-a-failed-hypothesis
9. https://reasonandscience.catsboard.com/t1438-hexameric-helicases-some-of-the-most-complex-machines-on-earth
10. https://reasonandscience.catsboard.com/t2039-the-interdependent-and-irreducible-structures-required-to-make-proteins
11. https://reasonandscience.catsboard.com/t2984-error-check-and-repair-during-messenger-rna-translation-in-the-ribosome-by-chance-or-design

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233My articles - Page 10 Empty Re: My articles on Sat Aug 01, 2020 7:29 am

Otangelo


Admin
Little science takes you away from God. But more of it, takes you to HIM. Louis Pasteur.

Romans 3:4 let God be true, but every man a liar

If there is one versicle in the New Testament, which has found its confirmation in an amazing manner, it is Pauls well-known observation in Romans 1.19-22.

For what can be known about God is plain to them because God has shown it to them. 20 For his invisible attributes, namely, his eternal power and divine nature, have been clearly perceived, ever since the creation of the world,7 in the things that have been made. So they are without excuse. 21 For although they knew God, they did not honor him as God or give thanks to him, but they became futile in their thinking, and their foolish hearts were darkened. 22 claiming to be wise, they became fools,

i hear frequently the claim by atheists, that all natural phenomena have always found a natural explanation. There is nothing farther from the truth. Exactly the opposite is the case. The more science investigates, the more it discovers that all natural phenomena cannot be explained by natural means.

Eliminative induction is based on the fact that its competitors are false. Materialism explains basically nothing consistently in regards to origins but is based on unwarranted consensus and scientific materialism, a philosophical framework, that should never have been applied to historical sciences. Evidence should be permitted to lead wherever it is. Also, eventually, to an intelligence agency as the best explanation of origins.

And intelligent design wins based on abductive reasoning, using inference to the best explanation, relying on positive evidence, on the fact that basically all-natural phenomena demonstrate the imprints and signature of intelligent input and setup. We see an unfolding plan, a universe governed by laws, that follows mathematical principles, finely adjusted on all levels, from the Big Bang, to the earth, to permit life, which is governed by instructional complex information stored in genes and epigenetically, encoding, transmitting and decoding information, used to build, control and maintain irreducible complex and interdependent cell factory parks, and a wide range, millions of species, of unimaginably complex multicellular organisms.

There is no evidence that we can exist without God.

The universe cannot create itself, nor can it be eternal.

The universe obeys mathematical laws; they are like a hidden subtext in nature. Mathematics is always invented and does not emerge from chaotic coincidence.

That a lucky accident finely tuned it on a razor's edge to make stars, essential for life, is a chance of one in 10^209 ( a vanishingly small number ) Chance practically zero.

Life cannot come from non-life.

There is no evidence that the four basic building blocks of life emerged randomly on the early earth.

There was no selection process to select the four nucleobases, nor the 20 amino acids, amongst hundreds extant on the early earth.

There is no known possible route from random molecules to the extremely complex molecular machinery, and chemical factory, producing the basic building blocks of life.

Biological cells require the basic building blocks, energy in the form of ATP, and codified instructional complex information, stored in a minimal genome of 1,300,000 nucleotides coding for about 1300 proteins. Chance to get those randomly is 1 in 10^700.000. There are 10^80 atoms in the universe.

Cells are interdependent and irreducible complex ( a minimal genome, proteome, and metabolome size are required to give life a first go ).

Biodiversity cannot be explained by evolution. Organismal complexity is due to preprogrammed instructional complex INFORMATION encoded in various genetic and epigenetic languages and communication by various signaling codes through various signaling networks.That brings us to the origin by an intelligent designer.

The Fossil record does not support evolution.

Conscience and personality can only come from conscience and personality.

Objective moral values exist, they cannot come from matter

Nature's Robots point to design

1. Machines, robots, fully automated manufacturing production lines, transport carriers, turbines, transistors, computers, and factories are always set up by intelligent designers.

2. Science has discovered, that cells are literally chemical nano factories, that operate based on molecular machines, protein robots, kinesin protein carriers, autonomous self-regulated production lines, generate energy through turbines, neuron transistors, and computers.

3. Therefore, most probably, Cell factories containing all those things are the product of an intelligent designer.

https://reasonandscience.catsboard.com/t2978-nature-s-robots-point-to-design

I don't choose to be a theist, I just can not force my brain to accept the claim that Biological cells which are a factory park of unparalleled gigantic complexity and purposeful adaptive design of interlinked high-tech fabrics, fully automated and self-replicating, directed by genes and epigenetic languages and signaling networks, could emerge by no guiding intelligence, but random unguided lucky accidents.


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234My articles - Page 10 Empty Re: My articles on Sat Aug 01, 2020 2:02 pm

Otangelo


Admin
Life depends on the structural complex arrangement using

- matter
- energy
- information

- Matter has to be arranged into basic building blocks of life, selected and joined amongst myriads of different atoms, and chemical molecules.

- Living systems need to recruit Gibbs free energy from its environment so as to reduce their own entropy. Simple chemicals can't self-organize into instructions for building hydroelectric dams (ATP synthase) producing energy-rich molecules, like ATP, essential for the supply of energy in all life-forms.

- Without information, the inflow of energy would not lead to self-organization. Information in this sense is more than information in the Shannon and Weaver sense; it is functional and can be thought of as information in both an “ instructional ” and “ control ” sense; it requires:

- the creation of codes, words, and languages to assign arbitrary values
- the creation of instructional complex information upon these codes
- the creation of information storage mediums, encoding, transmission, and decoding

Cells use sophisticated information selection ( the Gene regulatory network ) encoding and transcription ( DNA & RNA polymerase machines ) transmission (mRNA), and decoding ( Ribosome ) systems

All this is required to make complex structures — for example, enzymatic proteins — and metabolic pathways that productively channel the flow of energy both within an organism and between the latter and its environment.
If any of those ingredients is missing, there can be no life.

The making of repetitive building blocks for distant purposes by controlled instructional complex processes, and the arrangement of those thereof, using the purposeful flow of energy and higher layers of multidimensional information, to make complex machines, production lines, and self-replicating factories, is best explained by intelligent setup.

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The central problem to get the basic elements to make the building blocks of life on early earth

There is no evidence that the atoms required to make the basic building blocks of life were extant in a usable form on the early earth. A paper published by Nature magazine in 2016 claimed, that the foremost and only known nitrogen-fixing mechanism trough nitrogenase enzymes was extant in the last universal common ancestor. 1 But nitrogenase enzymes are of the HIGHEST complexity, truly marvels of nanomachinery, a molecular sledgehammer. 

The two main constituents of our atmosphere, oxygen (21%) and nitrogen (78%), both play important roles in the makeup of living things. Both are integral parts of the amino acids that join together in long chains to make all proteins, and of the nucleotides which do the same thing to form DNA and RNA. Getting elemental oxygen (O2) to split apart into atoms and take part in the reactions and structures of life is not hard; in fact, oxygen is so reactive that keeping it from getting into where it's not wanted becomes the more challenging job. However, elemental nitrogen poses the opposite problem. Like oxygen, it is diatomic (each molecule contains two N atoms) in its pure form (N2); but, unlike oxygen, each of its atoms is triple-bonded to the other. This is one of the hardest chemical bonds of all to break. So, how can nitrogen be brought out of its tremendous reserves in the atmosphere and into a state where it can be used by living things?

It is claimed that mineral-catalyzed dinitrogen reduction might have provided a significant source of ammonia to the Hadean ocean. But, there is a huge gap to go from such scenario to the ammonia production through nitrogenase enzymes. 

The chief enzyme is nitrogenase. With assistance from an energy source (ATP) and a powerful and specific complementary reducing agent (ferredoxin), nitrogen molecules are bound and cleaved with surgical precision. In this way, a ‘molecular sledgehammer’ is applied to the NN bond, and a single nitrogen molecule yields two molecules of ammonia. The ammonia then ascends the ‘food chain’, and is used as amino groups in protein synthesis for plants and animals. This is a very tiny mechanism but multiplied on a large scale it is of critical importance in allowing plant growth and food production on our planet to continue. 1

One author summed up the situation well by remarking, ‘Nature is really good at it (nitrogen-splitting), so good in fact that we've had difficulty in copying chemically the essence of what bacteria do so well.’ If one merely substitutes the name of God for the word 'nature', the real picture emerges.


The second problem is how to fix carbon dioxide to make glucose. The ultimate origin of  Glucose - sugars is a huge problem for those who believe in life from non-life without requiring a creator. In order to provide credible explanations of how life emerged, a crucial question must be answered: Where did Glucose come from in prebiotic earth? The source of glucose and other sugars used in metabolic processes would have to lie in an energy-collecting process. Without some means to create such sugar, limitations of food supply for metabolic processes would make the origin of life probably impossible. Sugars are by far the most attractive organic energy substrate of primitive anaerobic life, because they are able to provide all the energy and carbon needed for the growth and maintenance of the first organism.  

The hypothesis is that an ensemble of minerals that are capable of catalyzing each of the many steps of the reverse citric acid cycle was present anywhere on the primitive Earth, or that the cycle mysteriously organized itself topographically on a metal sulfide surface.  The lack of a supporting background in chemistry is even more evident in proposals that metabolic cycles can evolve to “life-like” complexity. The most serious challenge to proponents of metabolic cycle theories—the problems presented by the lack of specificity of most nonenzymatic catalysts—has, in general, not been appreciated. If it has, it has been ignored. Theories of the origin of life based on metabolic cycles cannot be justified by the inadequacy of competing theories: they must stand on their own.

But even, if, let's suppose, somehow, carbon fixation would have started on metal sulfide surface, there is an unbridgeable gap from that kind of prebiotic self-organization and carbon production, to even the most simple enzymatic carbon fixation pathway, used in anaerobic bacteria. the reductive tricarboxylic acid cycle rTCA is claimed to be the best candidate. That cycle requires nine sophisticated enzymes, some with complex molybdenum co-factors, which also have to be synthesized in highly ordered sequential multistep production pathways by various enzymes. How did that come to be without evolution? 3

An illustration: On the one side, you have an intelligent agency based system of the irreducible complexity of tight integrated, information-rich functional systems that have ready on hand energy directed for such, that routinely generate the sort of phenomenon being observed.  And on the other side imagine a golfer, who has played a golf ball through a 9 hole course. Can you imagine that the ball could also play itself around the course in his absence? Of course, we could not discard, that natural forces, like wind, tornadoes, or rains or storms could produce the same result, given enough time.  the chances against it, however, are so immense, that the suggestion implies that the non-living world had an innate desire to get through the 9 hole course. 4


Outlining just two elements demonstrates the size of the problem. But overall metabolism is based on seven non-metal elements, H, C, N, 0, P, S, and Se. With these elements, all the major polymers of all cells are made. Hence the major metabolic pathways involve them. In total, over 20 different elements, including heavy elements, like molybdenum, are absolutely essential for life to start.

The emergence of concentrated suites of just the right mix thus remains a central puzzle in origin-of-life research. Life requires the assembly of just the right combination of small molecules into much larger collections - "macromolecules" with specific functions. Making macromolecules is complicated by the fact that for every potentially useful small molecule in the prebiotic soup, dozens of other molecular species had no obvious role in biology. Life is remarkably selective in its building blocks, whereas the vast majority of carbon-based molecules synthesized in prebiotic processes have no obvious biological use. 5

1. https://reasonandscience.catsboard.com/t1585-nitrogenase
2. http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0060018
3. https://reasonandscience.catsboard.com/t1468-irreducible-complexity-the-existence-of-irreducible-interdependent-structures-in-biology-is-an-undeniable-fact#2133
4. https://reasonandscience.catsboard.com/t2419-where-did-glucose-come-from-in-a-prebiotic-world#6109
5. https://reasonandscience.catsboard.com/t2590-origins-what-cause-explains-best-our-existence-and-why#5811

https://reasonandscience.catsboard.com/t2437-essential-elements-and-building-blocks-for-the-origin-of-life#7789

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236My articles - Page 10 Empty Re: My articles on Wed Aug 05, 2020 7:23 am

Otangelo


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Answering the questions about how cells, tissues, and organisms form, precedes the question of how they can change and morph ( IF so) from one species to another on a first-degree speciation level, where novel organismal features arise, like wings, eyes, ears, legs, arms, and so forth. The fact is, that science is still FAR from being able to answer that question.

At least 23 epigenetic codes and languages are scientifically known. They all contribute to organismal development in a decisive way.

Search, Google, and try to find a science paper that shows the breaking of just one of those codes, and you will find NO answer to that question. Science has NO CLUE about how they are stored, nor the codification language, nor the cipher. Science knows that they exist through experimental tests, but deeper details are not known.

The naive view by uninformed people is that evolution is a fact and that microevolution leads to macroevolution, and that genes are enough to explain phenotype and physiological form. That is, frankly spoken, just false. Variation within species on a second-degree level, that leads even to speciation where inbreeding is not further possible, is not evidence of evolution, but pre-programmed adaptation, which is life essential.

When life started, adaptation had to be fully operational, otherwise, the organism would soon die. That explains why very varied organismal forms within species can arise within a few generations. Why artifical breeding can produce a danish dog, and a chihuahua, I outline the mechanisms involved here:

Why Darwin's theory of evolution does not explain biodiversity
https://reasonandscience.catsboard.com/t2623-why-darwins-theory-of-evolution-does-not-explain-biodiversity

We know as a fact, that common descent is a failed hypothesis:

Common descent, the tree of life, a failed hypothesis
https://reasonandscience.catsboard.com/t2239-evolution-common-descent-the-tree-of-life-a-failed-hypothesis

That, however, does not explain BY FAR, the rise of multicellular complexity, and biological variation of species. For that, the molecular landscape has to be fare more complex and involves many different mechanisms on an intra and extracellular level. The challenge is nothing short of phenomenal, and i have no idea, how unguided evolutionary mechanisms could account for the specification of even one of the trillions of cells based on hundreds of different cell types, that is:

1. Cell fate determination and differentiation ( phenotype, or what cell type each one will become )
2. Cell morphology and shape
3. Cell size
4. Precisely how many new cell types must be produced for each tissue and organ?
5. The specific function of each cell
6. Position and place in the body. This is crucial. Limbs like legs, fins, eyes etc. must all be placed at the right place.
7. How it is interconnected with other cells,
8. What communication it requires to communicate with other cells, and the setup of the communication channels
9. What specific sensory and stimuli functions are required and does it have to acquire in regard to its environment and surroundings?
10. What specific new regulatory functions it acquires
11. When will the development program of the organism express the genes to grow the new cells during development?
12. Changes in the composition of the cell membrane or secreted products.
13. Specification of the cell-cell adhesion and which ones will be used in each cell to adhere to the neighbor cells ( there are 4 classes )
14. Apoptosis: programming of the time period the cell keeps alive in the body, and when is it time to self-destruct and be replaced by newly produced cells of the same kind
15. Set up its specific nutrition demand
16. Number of cell divisions
17. Cell shape changes
18. Cell movement
19. Cell growth

Just the specification of individual cell morphology requires a myriad of different intracellular mechanisms, that work in an interdependent and synergetically manner together.

We know that life exists in interdependence with Viruses, which regulate ecologically the balance of different bacterial species. But Viruses are AMAZINGLY diversified and use many replication machineries that diverge essentially from how life replicates. These machineries as well had to be set up just right, in order for Viruses to be able to replicate, using bacterias as hosts.

There could not have emerged just one single progenitor ancestor cell, but a community of different bacterias and archaea prokaryotic cells would have been required, working in an interdependent relationship.

Bacterias have essential ecological significance and are necessary for a balanced ecological system, where all energy cycles work interdependently together. That forms another catch22 situation, to name:

Bacterias are an integral part of the energy cycles, which fix nitrogen, carbon dioxide, and make life-essential minerals available as nutrients for all life forms. But prokaryotes DEPEND on these energy cycles to obtain the essential organic elements, and minerals, to survive. What came first?

And ecology depends on an interdependent relationship of Viruses with bacterias, to maintain ecological homeostasis. That demonstrates, that the evolutionary narrative is false.

Every life form, and Viruses, had to emerge all at once, establishing the ecological environment, permitting the flourishing of life right from the start. That all points to a sudden appearance, all at once, of the living.

The Bible and Genesis are confirmed by what the scientific evidence has unravelled. Gradative evolutionary scenarios do not fit, and can be rejected based on the exposed above.

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The code of life, and minimal information to start life: By design, or not?

https://reasonandscience.catsboard.com/t2061p225-my-articles#7881

The base sequences in DNA and amino acids in proteins have functional specificity. The term “information” as used in biology refers to two real and contingent properties: complexity and specificity which bears functionality. In other words, the DNA nucleobase sequence prescribes, specifies, instructs how to build and join correctly amino acids, resulting in complex polymer macromolecules that fold into correct 3D folds, that bear machine-like functions.

Since the correlation confers not simply subjective meaning, DNA cannot be understood simply as a metaphor in biology. Where it refers to complex functional instructional specificity, it defines a feature of living systems that calls for an explanation every bit as much as, say, a mysterious set of inscriptions on the hieroglyphs on an ancient Egyptian inscription. Saying that it is a true code involves the idea that the code is free and unconstrained; any of the four bases can be placed in any of the positions in the sequence of bases. Their sequence is not determined by the chemical bonding. There are hydrogen bonds between the base pairs and each base is bonded to the sugar-phosphate backbone, but there are no bonds along the longitudinal axis of DNA. The bases occur in the complementary base pairs A-T and G-C, but along the sequence on one side, the bases can occur in any order, like the letters of a language used to compose words and sentences.

To further illustrate what is meant by a true code, consider the magnetic letters fixed to a magnetic board. The letters are held to the board by the magnetic forces, but those forces do not impose any specific ordering of the letters. The letters can be arranged to spell out a meaningful message in the English language (code) or to form a meaningless sequence like the one at the bottom.

The genetic code defines how a three-nucleotide codon specifies a single amino acid which will be added next during protein synthesis. Most genes are encoded with a single scheme, which is the RNA codon table, often referred to as the canonical or standard genetic code. It is what determines a protein's amino acid sequence. Codons consist of three DNA bases. If amino acids were randomly assigned to triplet codons, there would be 1.5 × 10^84 possible genetic codes. The origin of this assignment coding principle is a scientific mystery, since the only plausible, possible, and probable mechanism capable to do the assignment, a mind, is excluded a priory by modern science as a permissible explanation.  

Origin and evolution of the genetic code: the universal enigma
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3293468/

Let us suppose that assignment was a frozen accident, and we had in a miraculous manner a genetic code, assigning tri-nucleotide sequences for amino acids. How would there suddenly appear millions of sequences frozen in codon sequences, hypothetically assigned to a selected set of 20 amino acids? Consider, that there was no machinery to transcribe nor translate the code into amino acid sequences.

But let us go further, and suppose all the machinery was set and prepared to go, and do its job.

With four possible bases, the three nucleotides can give 4^3 = 64 different possibilities, 61 coding codons, and 3 start and stop signs, and these combinations are used to specify the 20 different amino acids used by living organisms. Now let us suppose, using an illustration and analogy, we had millions of 3 digit master locks, 64 different ones, each with a correct combination set useful to assign an amino acid, already locked up, for each of the 61 to specify one of the 20 amino acids used in life. To specify a protein with 400 amino acids having a sequence which would be functional, and permit the sequence to fold into a 3D form, we would need to line up 400  3 digit master locks in the right sequence. In EACH of the 400 positions, there would be 64 different 3 digit master locks to select from. That would give us the combinatorial possibilities of one chance in 64^400  or one chance in 10^153. If we posit that a minimal free-living cell had a proteome consisting of 1300 proteins, then the chance to get that right would be one chance in 10^200,000.  A clearly astronomical number, in the realm of the absolutely impossible.

There are multiple problems here. Starting first with the set up of the genetic code, secondly, freeze it to have triplets that assign to amino acids, and then join triplet combinations to have a functional sequence that would translate into sequencing amino acids, that would fold into functional 3D form. Not considering the fact, that the hardware would somehow also be required to emerge. We can safely say, that this scenario is too unlikely to happen purely by blind chemical forces. They could never have accomplished this challenging task. Intelligent design by a designer with foresight, is absolutely necessary to come up with this exquisitely engineered marvellous molecular arrangement

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238My articles - Page 10 Empty Re: My articles on Thu Aug 20, 2020 3:09 pm

Otangelo


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Many atheists demonstrate a faulty understanding of how things in nature work.

Repeatedly, i have heard atheists say: The Origin of Life depends just on chemicals. It's basically chemical reactions that over time increased complexity. That is a foolish simplification. Life depends on three basic things which are essential: Energy, matter, and information. While atheists are used to thinking that we are the simpletons, I regard is as more and more important to break down what happens in nature into analogies and a language, that everyone can understand, in order to explain concepts that are implemented in such a complex manner that science is still far from fully understand and describe what we see and observe in the natural world.

One common misconception is that natural principles are just discovered, and described by us. Two cans with Coca Cola, one is normal, the other is diet. Both bear information that we can describe. We describe the information transmitted to us that one can contain Coca Cola, and the other is diet. But that does not occur naturally. A chemist invented the formula of how to make Coke, and Diet Coke, and that is not dependent on descriptive, but PREscriptive information. The same occurs in nature. We discover that DNA contains a genetic code. But the rules upon which the genetic code operates are PRE - scriptive. The rules are arbitrary. The genetic Code is CONSTRAINT to behave in a certain way. Chemical principles govern specific RNA interactions with amino acids. But principles that govern have to be set by? - yes, precisely what atheists try to avoid at any cost: INTELLIGENCE. There is no physical necessity, that the triple nucleotides forming a Codon CUU ( cytosine, uracil, uracil ) are assigned to the amino acid Leucine. Intelligence assigns and sets rules. For translation, each of these codons requires a tRNA molecule that has an anticodon with which it can stably base pair with the messenger RNA (mRNA) codon, like lock and key. So there is at one side of the tRNA the CUU anticodon sequence, and at the other side of the tRNA molecule, there is a site to insert the assigned amino acid Leucine. And here comes the BIG question: How was that assignment set up? How did it come to be, that tRNA has an assignment of CUU anticodon sequence to Leucine? The two binding sites are distant one from the other, there is no chemical reaction constraining physically that order or relationship. That is a BIG mystery, that science is attempting to explain naturally, but without success. Here we have the CLEAR imprint of an intelligent mind that was necessary to set these rules. That led Eugene Koonin to confess in the paper: "Origin and evolution of the genetic code: the universal enigma" : It seems that the two-pronged fundamental question: “why is the genetic code the way it is and how did it come to be?”, that was asked over 50 years ago, at the dawn of molecular biology, might remain pertinent even in another 50 years. Our consolation is that we cannot think of a more fundamental problem in biology.

In the genetic code, there are 4^3 = 64 possible codons (tri-nucleotide sequences). Atheists also mock and claim that it is not justified to describe the genetic code as a language. But that is also not true. In the standard genetic code, three of these 64 mRNA codons (UAA, UAG and UGA) are stop codons. These terminate translation by binding to release factors rather than tRNA molecules. They instruct the ribosome to either start or stop polymerization of a given amino acid strand. Did unguided natural occurrences suddenly, in vast sequence space of possibilities, find by a lucky accident the necessity that a size of an amino acid polymer forming a protein requires a defined limited size that has to be INSTRUCTED by the genetic instructions, and for that reason, assigned release factors rather than amino acids to a specific codon sequence, in order to be able to instruct the termination of a amino acid string? That makes, frankly, no sense whatsoever. Not only that. This characterizes factually that the genetic code IS a language. That's described in the following science paper: The genetic language: grammar, semantics, evolution 2
The genetic language is a collection of rules and regularities of genetic information coding for genetic texts. It is defined by alphabet, grammar, collection of punctuation marks and regulatory sites, semantics.

1. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3293468/
2. http://www.ncbi.nlm.nih.gov/pubmed/8335231

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Origin of life research faces three major problems

1. The making of the basic building blocks of life, and complexification
At its most fundamental level, life is made of matter. In a putative prebiotic soup or hydrothermal vents, there is the random chaotic floating around of all sorts of chemicals and molecules in an aqueous environment, in non-purified and racemic form. In order to start the trajectory to complexification to get supposed protocells, and continuing, through chemical evolution, getting to a last universal common ancestor, capable of starting self-replication, and evolution, not only would the basic building blocks have to be purified, but also concentrated in sufficient quantity at the building site. The concentration would have to go hand in hand with sorting out molecules that are useless and keeping molecules used in life. There was no such mechanism on the early earth. There would have to be as well an enormously distant and steep trajectory from the prebiotic synthesis of those basic building blocks ( through electric discharges, synthesis on clay, metals, etc ), to the production performed in a superb manner by modern cells, which use extremely complex metabolic pathways, consistent of highly intricate, veritable molecular production lines, full of marvelous molecular machines, driven by energy in the form of ATP molecules, which require carefully crafted energy gradients and awe-inspiring nano energy turbines to be energetically charged, working in a robot-like fashion, producing all chemicals that life needs.  
 
Lynn Margulis: To go from a bacterium to people is less of a step than to go from a mixture of amino acids to a bacterium. 

Further problems arise by the fact that these 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.

2. Randomization of molecules, and the energy problem
Virtually every task performed by living organisms requires energy. Complexification would not get "off the hook" based on thermodynamic considerations.  Maintenance of the low entropy state of living systems requires the persistent infusion of energy, first, to enable the system to maintain its complex organization and resist dissipation toward randomness. But if there even were a trajectory to get the basic building blocks of life prebiotically: 

As Steve Benner noted: Systems, given energy and left to themselves, DEVOLVE to give uselessly complex mixtures, “asphalts”.  the literature reports (to our knowledge) exactly  ZERO CONFIRMED OBSERVATIONS where “replication involving replicable imperfections” (RIRI) evolution emerged spontaneously from a devolving chemical system. it is IMPOSSIBLE for any non-living chemical system to escape devolution to enter into the Darwinian world of the “living”. Such statements of impossibility apply even to macromolecules not assumed to be necessary to start evolution.

Energy flow in non-living systems tends to result in greater disorder among all elements of the system.  The energy transformations of living systems serve primarily to harvest and store the levels of free energy necessary for maintaining the highly ordered structure of the organism and performing the work that living cells carry out. The net effect for living systems, in contrast to that for non-living systems, is to maintain and often increase order at local levels and on microscopic scales. The function of a living organism depends critically on precisely how it is put together. Its component parts function in a coordinated manner, to generate a complex array of emergent properties, both structurally and functionally. The second consequence of biological energy transformations is to create one or more additional microenvironments within the natural environment.  PH, solute composition, and structural complexity of the living cell are maintained at levels different from the extracellular environment because of the autonomous functions carried out by the cell, but not in the abiotic environment surrounding the cell.  There is a dual requirement of living systems: to resist an increase in entropy and to perform work. Both requirements are essential for the definition of a living entity. Any fabrication or machine is, for the time being, at a lower state of entropy than, and in disequilibrium with, its environment. 


3. The information problem
Norbert Weiner - MIT Mathematician - Father of Cybernetics "Information is information, not matter or energy. No materialism which does not admit this can survive at the present day." 
For explaining the origin of life we must also explain the origin of the genetic cipher/translation, from digital ( DNA / mRNA ) to analog ( Protein ), the origin of the epigenetic codes ( modern cells use over 20),  the specified instructional complex codified information contained in each life form's unique DNA and RNA, the origin of the network that orchestrates gene expres​sion( the gene regulatory network) through transcriptional regulation, the origin of the information transmission system, that is the genetic code itself, encoding, transmission, decoding, and translation, and furthermore, the origin of the codes, signaling and information, for correct direction of proteins to the final destination in the cell. When no prescriptive information exists it is impossible for information, languages, and information transmission systems to arise naturally in a mindless world. Instructional Information is more than just matter and independent of its storage medium. Like a language has a sender and a receiver who both understand the message and act according to it, the medium can be of various sorts, like a piece of paper, written on a sand dune, etc.  All communication and data processing, as is also done in the cell, is achieved through the use of symbols. When a computer processes code it has to decode it in order to convert the code into the corresponding action. Hubert P. Yockey wrote: A satisfactory scenario for spontaneous biogenesis requires the generation of “complexity” not “order”. The probability of selecting the right sequence of cytochrome c at random is about 2·1 ×10^65.  Belief in currently accepted scenarios of spontaneous biogenesis is based on faith, contrary to conventional wisdom.

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How God displays his extraordinary and masterful creative power. 

Formation of Deoxyribonucleotides
https://reasonandscience.catsboard.com/t2028-the-dna-double-helix-evidence-of-design#3432

DNA is the core of life on Earth, every known living organism is using DNA as their genetic backbone. DNA is so precious and vital to eukaryotic cells that its kept packaged in the cell nucleus, it's being copied but never removed because it never leaves the safety of the nucleus.

One of the key differences between DNA and RNA is at the two prime positions on ribose (2'), the "backbone" of RNA and DNA,  RNA has a hydroxyl (-OH) group attached ( It contains an oxygen atom bonded to a hydrogen atom) that DNA does not. This gives DNA its name: DNA stands for de ( without ) oxy ( oxygen )ribonucleic acid ( Deoxyribonucleotide ). With the removal of the oxygen atom, DNA has only a hydrogen atom.  That, amongst other minor differences, permits  DNA and RNA to play very different roles from one another in modern cells.

RNA and DNA are BOTH life-essential. DNA carries genetic instructions for the development, functioning, growth, and reproduction of all known organisms and many viruses. messenger RNA (mRNA) is the primary transcript that is translated by the Ribosome, and a protein is synthesized.

The absence of this single oxygen atom is the key for robustness and stability and permits to extend DNA's longevity, and is life-essential. The primary advantage of DNA over RNA as genetic material is the greater chemical stability of DNA, allowing much larger genomes based on DNA. When the 2' Oxygen is absent in deoxyribose, the sugar molecule is less likely to get involved in chemical reactions ( the aggressive nature of Oxygen in chemical reactions is famous). So by removing the Oxygen from the deoxyribose molecule, DNA avoids being broken down. In an RNA's point of view, the Oxygen is helpful, unlike DNA, RNA is a short-term tool used by the cell to send messages and manufacture proteins as a part of gene expression.

In short: The ribose sugar is placed in RNA for easily decomposing it and DNA uses deoxyribose sugar for longevity. The RNA molecule, with autoreplicative capacity, as a primary primitive molecule for the genetic information storage, has its shortcomings precisely for not being stable, and unable to form long information-bearing strands. 

The remarkable and extraordinary enzyme which replaces the OH group at C2′ of the ribose moiety of the four common ribonucleotides with hydrogen is Ribonucleotide reductase. This is a macromolecular machine of exceptional features and complexity. It is one of the most challenging and complex enzymes.  The iron-dependent enzyme is essential for DNA synthesis. It is one of the most essential enzymes of life. 

Three different RNR classes are known, with little apparent similarity between them in terms of the primary protein sequence (approximately 10–20% similarity). 

Question: How can it be explained proposing natural mechanisms, that this ultracomplex enzyme performs the same enzymatic reaction in three different ways? To claim common ancestry, in this case, is an ad-hoc assertion. Truth said, science is unable to infer a reasonable scenario out of the evidence, and all it can do, is resort to made-up stories, which bear no credibility. The best and straightforward explanation is that a creator made RNR's, and equipped each of them with different ways to perform the same function. Of course, we can ask, why did he do so. If no apparent mechanistically useful explanation exists, I infer that God wanted to show us his exuberant creativity and capacity. 
 
All classes of RNR share two remarkable features worth mentioning:

1. The polypeptide chain of the active enzyme harbors remarkably a free radical amino acid residue ( a molecular species capable of independent existence that contains an unpaired electron in an atomic orbital ) that participates in the catalytic process; the mechanism for radical generation sets the classes apart.  It is remarkable that RNR uses some of the most potent metals in redox chemistry. All RNRs use radical chemistry to catalyze this challenging reaction.
2. The specificity of the four ribonucleotides is tightly controlled by allosteric effects.

RNRs are mechanistically fascinating because of their free radical chemistry, unusual metallocofactors, and complex regulatory mechanisms.

Recently, a science paper reported that scientists were able to visualize the complex molecular dance that allows the enzyme to transport the catalytic “firepower” from one subunit to the next, in order to generate DNA building blocks. This firepower is derived from a highly reactive unpaired electron (a radical), which must be carefully controlled to prevent damage to the enzyme. RNR does the equivalent of playing with fire without getting burned.1


Question: How did this enzyme acquire its ability to carefully control the reaction, and prevent damage to the enzyme? Trial and error? Was it damaged innumerable times, until the right configuration was sorted out, and the reaction was actually able to start its job in the right way?

It is crucial that these dNTP pools are carefully balanced since mutation rates increase when dNTP levels are either unbalanced or elevated. RNR is the major player in this homeostasis, and with its four different substrates, four different allosteric effectors g and two different effector binding sites a, it has one of the most sophisticated allosteric regulations known today.

How and when ribonucleotide reduction emerged is a question that is intimately associated with the transformation of  RNA to DNA, since it is the only known de novo mechanism for deoxyribonucleotide dNTP synthesis, and, as such, had to be fully operational when life kick-started. The mechanism has been deemed unlikely to be catalyzed by a ribozyme, creating an enigma regarding how the building blocks for DNA were synthesized at the transition from RNA to DNA-encoded genomes. 

That brings us to the classic chicken and egg, catch22 situation.  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 proposals and any possibility of transition from  RNA to DNA world scenarios.

RNR plays a critical role in regulating the total rate of DNA synthesis so that DNA to cell mass is maintained at a constant ratio during cell division and DNA repair.
RNR's activity is highly transcriptionally regulated and cell phase-dependent. To avoid imbalanced levels of Nucleoside triphosphates (dNTPs) and the increased mutation rates that are the inevitable consequences of this RNRs are tightly controlled through transcriptional and allosteric regulation, subcellular compartmentalization, and small protein inhibitors. Allosteric regulation ( which is the regulation of an enzyme by binding an effector molecule at a site other than the enzyme's active site) of RNR's affects both substrate specificity and overall activity. That ensures balanced levels of the four deoxyribonucleotides dNTPs in the cell.

My comment: Ensuring balanced levels of the four deoxyribonucleotides dNTPs in the cell is essential to avoid high mutation rates which would result in cell death. How could such a highly complex, orchestrated, and regulated process have emerged prebiotically, in a stepwise, Darwinian evolution fashion? In order to have this balanced supply, this exquisitely engineered molecular machine had to be fully operational to do its job.

This is truly awe-inspiring:
Ribonucleotide reductases use Quantum mechanics for repair when something goes havoc during the reduction process.

Class one ( one of the three classes) uses a diiron-centered tyrosyl radical cofactor (Fe2–•Y122) that is essential for catalysis. Once the nucleotide substrate binds on the second subunit of the RNR enzyme, and a mistake occurs, the diiron(III)–tyrosyl-radical Tyr is reduced by an exogenous small molecule, and a repair system regenerates the tyrosyl radical cofactor.

My comment: to draw a parallel to our world. If a part in the engine of car brakes, we have to visit a mechanic which has to discover what has broken and has to fix it. This enzyme has already an inbuilt repair mechanism to perform the repair !! It is evident that God knew beforehand, what could go wrong, and installed from the beginning a solution to fix an eventual problem!!

Not only is there a repair mechanism installed, but the distance from the reaction center, where the nucleotides are reduced, the diiron cluster is 35 angstroms away. In the molecular world, a considerable distance. In order to overcome the distance, Proton-coupled electron transfer (PCET) is used.  This distance, 35-40 angstroms from the first subunit to the second, is roughly 10 times farther than the average radical transfer. The radical must then travel back to its starting place and be stored safely, all within a fraction of a second before the enzyme returns to its normal conformation.

Furthermore, a well-coordinated proton exit channel is essential. Not only that, this is intrinsically a quantum mechanical effect as both the electron and proton tunnel. In doing so, the enzyme imparts exquisite thermodynamic and kinetic controls over radical transport and radical-based catalysis at cofactor active sites. The enzymes speed up the reaction one trillion times compared to a non-enzymatic reaction.

My comment: All this hyper-sophisticated and elaborated molecular technology is present just in ONE enzyme which is responsible just for one tiny step of many others which are required to make the most basic and fundamental building block of life, DNA.  No wonder is this enzyme being studied intensively since it was discovered in 1951, and new surprises come to light even after 70 years .... There was no evolution around prior DNA replication and DNA. We are describing an enzyme, which is fundamental, and had to emerge prior when life began. The only alternative to explain its emergence, once design by a super hyper-intelligent agency is excluded, is luck. A random, unguided undirected accident.

Think about it. CRITICALLY. 

The molecular world of biochemistry is the place where God displays his unfathomable brilliance, ingeniosity, and limitless intelligence in a formidable way. There, we see carefully crafted solutions and planned inventions that man never expected to find. Ribonucleotide reductase enzymes are masterpieces of God's creation. As is Deoxyribonucleotides (dNTPs), or DNA. Once taken a closer eye on it, we recognize that it is an awe-inspiring information-storage molecule that could never have emerged on early earth by chance. And RNR's testify it !!


a: In biochemistry , an effector molecule is usually a small molecule  that selectively binds to a protein and regulates its biological activity. In this manner, effector molecules act as ligands  that can increase or decrease enzyme activity , gene expression , or cell signaling . Effector molecules can also directly regulate the activity of some mRNA  molecules (riboswitches ). 59

1. https://news.mit.edu/2020/enzyme-square-dance-helps-generate-dna-building-blocks-0330

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Otangelo


Admin
I am having a lot of fun in my interaction on YouTube. The live chats are something relatively new for me. It isn't more than a month that I started The God-talk,

https://www.youtube.com/channel/UC0nEzsU2UOrx1eXGw-Kjw4w?view_as=subscriber

and there is a lot going on there. In yesterday afternoon's chat with Dimiter, I asked him about the transition and evolution of his peptide hypothesis with proto - translation, to a fully developed translation in modern cells. The first thing I remember that Dimiter replied, was: That's not a problem. And then started his explanation. I was thinking to myself: What the heck: That's not a problem? What is he talking about? That's a HUGE problem.

The Ribosome is one of the most complex macromolecule complexes known. We still do not have a full understanding of how it works, and the more science advances, the more fantastic molecular technology comes to light. To explain its origin is in my understanding a HUGE problem. Recently, John Maddox draw my attention to a recent science paper, Nervous-Like Circuits in the Ribosome come to light. I wrote an article based on that paper, which I post a resume and syllogism below.

There is another issue which I brought up in my talk with Dimiter, which problem he, in my opinion, downplays, and apparently sub estimates. That is the fact, that prior to tRNA's for example starting to have their function as adapter molecules in the orchestration of translation, they have to be synthesized. That is by no means an easy task. Its synthesis it as well complex, and the tRNA set would have had to co-evolve with the supposed addition of each triplet codons in the genetic code alphabet, in order to recognize each new genetic "word". How could the biosynthesis of tRNA's have emerged ( or evolved ), if tRNA's play only a role once they are incorporated and working in a joint venture together with all other players in translation ( mRNA, the genetic cipher, aminoacyl tRNA synthetases, the Ribosome, the Signal Recognition Particle )?

Not to mention, that each of those parts, in special the Ribosome, require as well extremely complex synthesis pathways ( the ribosome about 200  enzymes, scaffold-proteins, and about 75 co-factors in an extremely complex highly ordered, and orchestrated assembly process )?. How did all that come to be? In my opinion, this is an all or nothing business. A stepwise, gradual evolutionary emergence is not feasible ( and that's the only way materialists can explain its origin).  Yes, I am incredulous towards that hypothesis, and I think, I am justified to be so. What about you?

Btw. if you are not yet my Facebook friend, this is my profile link:
https://www.facebook.com/angelo.grasso.92317121

Origin of  translation of the 4 nucleic acid bases and the 20 amino acids, and the universal assignment of codons to amino acids
https://reasonandscience.catsboard.com/t2057-origin-of-translation-of-the-4-nucleic-acid-bases-and-the-20-amino-acids-and-the-universal-assignment-of-codons-to-amino-acids  

The interdependent and irreducible structures required to make proteins
https://reasonandscience.catsboard.com/t2039-the-interdependent-and-irreducible-structures-required-to-make-proteins  

Aminoacyl-tRNA synthetases
https://reasonandscience.catsboard.com/t3017-aminoacyl-trna-synthetases

Transfer RNA, and its biogenesis, best explained through design
https://reasonandscience.catsboard.com/t2070-transfer-rna-and-its-biogenesis  

Signal Recognition Particle: An essential protein targeting machine
https://reasonandscience.catsboard.com/t2651-signal-recognition-particle-an-essential-protein-targeting-machine  

Ribosomes amazing nanomachines
https://reasonandscience.catsboard.com/t1661-translation-through-ribosomes-amazing-nano-machines  

Error detection and repair during the biogenesis & maturation of the ribosome, tRNA's, Aminoacyl-tRNA synthetases, and translation: by chance, or design?
https://reasonandscience.catsboard.com/t2984-error-check-and-repair-during-messengerrna-translation-in-the-ribosome-by-chance-or-design  

Nervous-Like Circuits in the Ribosome come to light
https://reasonandscience.catsboard.com/t1661-translation-through-ribosomes-amazing-nano-machines#7900

1. The set up of a language, and upon it, the programming of a completely autonomous communication network, which directs the operation of a complex factory, which during operation error checks and performs repairs, to make specific purposeful products, is always the product of an intelligent agency.

2. Ribosomes are molecular factories with complex machine-like operations. They carefully sense, transfer, and process, continually exchange and integrate information during the various steps of translation, within itself at a molecular scale, and amazingly, even make decisions. They form complex circuits. They perform masterfully long-range signaling and perform information transfer between remote functional sites. They communicate in a coordinated manner, and information is integrated and processed to enable an optimized ribosome activity. Strikingly, many of the ribosome functional properties go far beyond the skills of a simple mechanical machine. They choreograph, collaborate, modulate, regulate, monitor the translation status, sensor quality, synchronize, and coordinate extremely complex movements, like rotations and elongations, even helped by external synchronization systems. to direct movements during translation. The whole system incorporates 11 ingenious error check and repair mechanisms, to guarantee faithful and accurate translation, which is life-essential.

3. The Ribosome had to be fully operational when life began. This means the origin of the Ribosome cannot be explained by Darwinian evolution. No wonder does science confess that the history of these polypeptides remains an enigma. But for us, theists, the enigma has an explanation: an intelligent cognitive agency, a powerful creator, God, through his direct intervention, wonderful creative force, and activity, created this awe-inspiring life-essential factory inside of many orders of magnitude greater cell factories, fully operational right from the beginning.

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242My articles - Page 10 Empty Re: My articles on Tue Sep 15, 2020 3:15 pm

Otangelo


Admin
The argument from integrated interdependent complexity

piston used in a car engine requires a complex fabrication process to be manufactured with the right shape, size, and materials. On its own, it bears no function. But in a car engine, it is fundamental. Without it, the engine will not work. Nobody would produce a piston without foreseeing where it would be employed and be used, and its function.

A protein requires a complex manufacturing process to be synthesized with the right shape, size, and materials. On its own, it bears no function. But in a living cell, many different proteins are fundamental. Without them, the cell cannot operate. Often, proteins work interdependently with other proteins in a production line like process, forming an integrated system, producing chemicals and molecules used in the cell.

Random molecules laying around on prebiotic earth do not have the "urge" to start chemical reactions, complexify and employ natural selection to sort out components that are useful for a future system with specific purposes of a higher order and complexity, where those proteins would only have use and work in a complex integrated manner after the completion of that much larger system. Furthermore, raw molecules rather decompose, rather than turn themselves into complex computers driving and controlling machines, turbines, energy plants, and factories.

In modern cells, the pathway or protein synthesis starts with the DNA molecule, and through the genetic code, an instructional blueprint is stored in DNA, which is transcribed in mRNA, and translated in the Ribosome to make proteins. That pathway was not existing on the early earth. I have yet to hear a reasonable suggestion of how the transition happened from random molecules laying around on a prebiotic earth or swimming in a prebiotic soup, or hydrothermal vents, to a fully developed protein synthesis pathway. Not to mention the gene regulatory network that orchestrates gene expression, and the pathway from the point when the protein comes out from the Ribosome until it is post-translationally modified, tagged, and the pathway to its final destination. Not to forget that the error check and repair mechanisms have to be explained, and as well the origin of all the molecular machinery to make the individual holo-enzymes, in special the Ribosome, the tRNA's, the aminoacyl tRNA synthetases, the signal recognition particle, which have to work together, and if one is missing, no deal. How did all this complexity take off the hook, starting with some random small peptides, forming accidentally on the early earth?

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