Intelligent Design, the best explanation of Origins

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Nothing exists outside of the Mind! God is Mind. Matter is an illusion of Consciousness.

http://reasonandscience.catsboard.com/t2061p100-my-articles#6037

Werner Heisenberg
“The atoms or elementary particles themselves are not real; they form a world of potentialities or possibilities rather than one of things or facts.” 3

I think that modern physics has definitely decided in favor of Plato. In fact the smallest units of matter are not physical objects in the ordinary sense; they are forms, ideas which can be expressed unambiguously only in mathematical language. 4

Of course, we all know that our own reality depends on the structure of our consciousness; we can objectify no more than a small part of our world. But even when we try to probe into the subjective realm, we cannot ignore the central order…In the final analysis, the central order, or 'the one' as it used to be called and with which we commune in the language of religion, must win out.

Sir James Hopwood Jeans
Today there is a wide measure of agreement, which on the physical side of science approaches almost to unanimity, that the stream of knowledge is heading towards a non-mechanical reality; the universe begins to look more like a great thought than like a great machine. Mind no longer appears as an accidental intruder into the realm of matter; we are beginning to suspect that we ought rather to hail it as a creator and governor of the realm of matter... 5

The tendency of modern physics is to resolve the whole material universe into waves, and nothing but waves. These waves are of two kinds: bottled-up waves, which we call matter, and unbottled waves, which we call radiation or light. If annihilation of matter occurs, the process is merely that of unbottling imprisoned wave-energy and setting it free to travel through space. These concepts reduce the whole universe to a world of light, potential or existent, so that the whole story of its creation can be told with perfect accuracy and completeness in the six words: ‘God said, Let there be light’.

Bernard d'Espagnat
"The doctrine that the world is made up of objects whose existence is independent of human consciousness turns out to be in conflict with quantum mechanics and with facts established by experiment."

Martin Rees
In the beginning there were only probabilities. The universe could only come into existence if someone observed it.

Freeman Dyson, Infinite in All Directions (1988), p. 18
What philosophical conclusions should we draw from the abstract style of the superstring theory? We might conclude, as Sir James Jeans concluded long ago, that the Great Architect of the Universe now begins to appear as a Pure Mathematician, and that if we work hard enough at mathematics we shall be able to read his mind. Or we might conclude that our pursuit of abstractions is leading us far away from those parts of the creation which are most interesting from a human point of view. It is too early yet to come to conclusions.

Physicists, especially the physicists of small things and microcosmic states, see matter and energy vanishing, virtual particles popping in and out of apparently 'nothing' and the indeterminacy of any material state. Some are beginning to see that information, that exists but has zero mass and carries zero energy, and therefore not material at all, is primary over both matter and energy and may even give rise to them. 6

What is energy? In physics, energy is the property that must be transferred to an object in order to perform work on, or to heat, the object

Wiki describes energy as " property" . Why is energy not simply the ' force ' of Gods word in action? they talk about an object. But matter is not an object. matter is energy.... 2

W.L.Craig: The quantum vacuum is not what most people envision when they think of a vacuum-that is, absolutely nothing. On the contrary, it's a sea of fluctuating energy, an arena of violent activity that has a rich physical structure and can be described by physical laws.

Space Is Not Empty, It’s Actually Full of Energy: The Quantum Vacuum

Quantum physicists discovered that physical atoms are made up of vortices of energy that are constantly spinning and vibrating, each one radiating its own unique energy signature. This is also known as "the Vacuum" or "The Zero-Point Field."

“A century from now, it will be well known that: the vacuum of space which fills the universe is itself the real substratum of the universe; vacuum in a circulating state becomes matter; the electron is the fundamental particle of matter and is a vortex of vacuum with a vacuum-less void at the center and it is dynamically stable; the speed of light relative to vacuum is the maximum speed that nature has provided and is an inherent property of the vacuum; vacuum is a subtle fluid unknown in material media; vacuum is mass-less, continuous, non viscous, and incompressible and is responsible for all the properties of matter; and that vacuum has always existed and will exist forever….Then scientists, engineers and philosophers will bend their heads in shame knowing that modern science ignored the vacuum in our chase to discover reality for more than a century.”

At the turn of the nineteenth century, physicists started to explore the relationship between energy and the structure of matter. In doing so, the belief that a physical, Newtonian material universe that was at the very heart of scientific knowing was dropped, and the realization that matter is nothing but an illusion replaced it. Scientists began to recognize that everything in the Universe is made out of energy. 1

What’s even more fascinating is that the “stuff” within this space can be accessed and used. This was experimentally confirmed when The Casimir Effect illustrated zero point or vacuum state energy, which predicts that two metal plates close together attract each other due to an imbalance in the quantum fluctuations.

Most of what we refer to as “reality” is actually something we can’t perceive with our physical senses!

Tapping the Zero Point Energy  Moray B. King




1. https://www.collective-evolution.com/2018/06/07/space-is-not-empty-its-actually-full-of-energy-the-quantum-vacuum/
2. https://en.wikipedia.org/wiki/Energy
3. http://quantumenigma.com/nutshell/notable-quotes-on-quantum-physics/
4. https://en.wikiquote.org/wiki/Werner_Heisenberg
5. https://en.wikiquote.org/wiki/James_Jeans
6. https://www.quora.com/What-did-Werner-Heisenberg-mean-when-he-said-%E2%80%9CThe-first-gulp-from-the-glass-of-natural-sciences-will-turn-you-into-an-atheist-but-at-the-bottom-of-the-glass-God-is-waiting-for-you%E2%80%9D

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102 Re: My articles on Thu Jul 05, 2018 6:42 am

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The amazing complexity to make DNA nucleobases

http://reasonandscience.catsboard.com/t2028-origin-of-the-dna-double-helix#3426

Both nucleobases, Pyrimidines, and Purines had to begin to be produced prior when life began since they make up DNA - the molecule that stores genetic information. That means as well, that all enzymes used in the pathway to make the bases had to be present prior the supposed Last Universal Common Ancestor ( that's a fairy tale anyway, but for the argument, it doesn't matter )  For pyrimidines, six synthesis manufacturing/biosynthesis steps are required, and for purines, eleven. 

The thrilling part is that just one of all these enzymes is staggeringly complex. David Goodsell writes: Aspartate carbamoyltransferase is fully as complex as any fine automobile in our familiar world. 

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 part. 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. And, just as manufacturers invest a great deal of research and time into the design of an automobile, enzymes like aspartate carbamoyltransferase are finely tuned.

Beside this enzyme, all others, almost 20, had to be produced prebiotically, and then interconnected like in a factory assembly line, to make DNA nucleobases !! 

There was no evolution. No natural selection. No mutations - nah nah  Charly won't provide the crutches to explain the feat.....

The only alternative to these biochemical processes would be, that the basic building blocks were readily available on a prebiotic earth. Glycine for instance is a indispensable substrate for purine nucleotide synthesis, and so - DNA - in cells. It  requires at least 5 biosynthetic steps and the respective enzymes to be synthesized. In a prebiotic earth, the only alternative would have been that glycine came from comets.

Comet contains glycine, key part of recipe for life 3
May 27, 2016
An important amino acid called glycine has been detected in a comet for the first time, supporting the theory that these cosmic bodies delivered the ingredients for life on Earth, researchers said Friday.
In addition to the simple amino acid glycine, the instrument also found phosphorus. The two are key components of DNA and cell membranes. "Demonstrating that comets are reservoirs of primitive material in the Solar System, and vessels that could have transported these vital ingredients to Earth, is one of the key goals of the Rosetta mission, and we are delighted with this result."

Panspermia, not a viable explanation for the OOL
http://reasonandscience.catsboard.com/t1362-panspermia#1926

Chemistry happens, and interesting molecules form in space; so what?  It’s not going to help the believers in naturalistic origin of life.  So they found glycine, the simplest and only non-chiral amino acid.  The biologists told the astronomers to look for life’s building blocks in space, because they were having such a hard time producing them on Earth.  They would need megatons of amino acids and nucleic acid bases to rain down on the Earth for any hope of getting successful concentrations, but then the precious cargo would be subject to rapid degradation by water, oxygen, UV light, and harmful cross-reactions.  Even then, they would be mixtures of left and right handed forms, with no desire nor power to organize themselves into astronomers who could invent weird science like this.
.
Following the unresolved issues of nucleotide biosynthesis
http://reasonandscience.catsboard.com/t2028-biosynthesis-of-the-dna-double-helix-evidence-of-design#3426

Glycine
http://reasonandscience.catsboard.com/t1740-origin-of-the-canonical-twenty-amino-acids-required-for-life#5731

While individual laboratory conditions could conceivably represent those of early Earth, many prebiotic ingredients mutually exclude one another. For example, two nucleotide bases (adenine and guanine) require freezing conditions for their synthesis, while two other nucleotide bases (cytosine and uracil) demand boiling temperatures. For all four building blocks to take shape at the same time, the prebiotic soup must simultaneously freeze and boil. 7

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103 Re: My articles on Thu Jul 05, 2018 8:58 am

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Mr.Nothing
Yesterday I asked my good old friend, his name is nothing, how he felt. He answered nothing. Then I asked him if he had creative powers. He answered nothing. Then I wanted to know if he maybe had something to do with the origin of multiverses. He, again, did not answer anything. So I began starting to feel upset, since my questions were ignored constantly. I made another attempt, and asked: Did you cause the vacuum to make virtual particles into existence? No answer. Did you eventually cause the Big Bang into being? no answer again. So I got reeeallly upset, and asked in an altered manner: Why do you not answer? DID YOU FINE TUNE OUR UNIVERSE? no answer again. Nothing, are you there? no answer again. I started to become hopeless, and made a last attempt: Nothing, did you scramble the prebiotic chemistry to see if some RNA molecule emerged? No answer again. So I said to myself: What an ignorant bastard, Mr. Nothing. Completely ignoring me, and answering - nothing.....

===============================================================================================================================================

Life is an all or nothing business

The purine base adenine is one of the four life-essential nucleobases used in DNA, the information storage molecule of the Cell, besides serving as the base for adenine triphosphate, ATP, the energy storage molecule of life.  While it is widely known how important DNA is to store information, less known is how complex the metabolic pathways are to synthesize the four nucleotides and bases used in DNA to form the genetic code.

Its formation derives from a complex pathway using atoms from the amino acids glycine, aspartic acid,  the coenzyme tetrahydrofolate, formate,  the amide group of glutamine, and Bicarbonate HCO-3. In order to recruit these starting materials, they need to be available through the metabolic network which must be fully set up, like the Krebs cycle and Glycolysis.  Adenine is synthesized in a complex biosynthesis pathway requiring at least 14 enzymes. 

Some of these enzymes are multifunctional enzymes. They do not only regulate the overall production rate, but the intermediate products of these multifunctional enzymes are not readily released to the medium but are channeled to the succeeding enzymatic activities of the pathway. Channeling increases the overall rate of these multistep processes and protects intermediates from degradation by other cellular enzymes.

Another smart feat is the fact that it is energetically costly to produce nucleotides from scratch. In order to economize, nucleotides are reconverted through various salvage pathways for re-use. 

Adenine is attached to a ribose sugar forming the nucleobase Adenosine, made up of three parts, the nucleobase, the ribose sugar, and one monophosphate group. 

In order to drive the energy demanding reactions of the enzymes to make adenosine monophosphate AMP, another well-known molecule is required, ATP.  ATP is the " energy currency " of most cellular reactions and contains the very own purine base adenine described above, and the sugar ribose which together forms the nucleoside adenosine. The difference to adenosine monophosphate is that ATP uses three phosphate groups linked by what is known as phosphoanhydride bonds. The breakup of these bonds during cell activity is what generates the energy used in all life forms. For this reason, ATP is a critically important macromolecule—arguably “second in importance only to DNA". In order to get three phosphate groups required in ATP, a second phosphate group has first to be attached to Adenosine monophosphate AMP through a remarkable enzyme, named  Adenylate-Kinase. 

Adenylate-Kinase converts one AMP with the use of ATP into two nucleoside diphosphate forms. The further step, oxidative phosphorylation,  is primarily responsible for the conversion of nucleoside diphosphate ADP into triphosphate forms, ATP through ATP synthase turbines in mitochondria, and photosynthesis. 

The job of Adenylate-Kinase is not only to add one phosphate group to produce Adenosine diphosphate,  but also constantly monitors phosphate nucleotide levels inside the cell, and plays an important role in cellular energy homeostasis. By continually monitoring and altering the levels of ATP and the other adenyl phosphates (ADP and AMP levels) adenylate kinase is an important regulator of energy expenditure at the cellular level. As energy levels change under different metabolic stresses adenylate kinase is then able to generate AMP; which itself acts as a signaling molecule in further signaling cascades. An article in Nature magazine reports its importance:

Adenylate Kinase (AK) is a signal transducing protein that regulates cellular energy homeostasis balancing between different conformations. An alteration of its activity can lead to severe pathologies such as heart failure, cancer and neurodegenerative diseases. Cellular homeostasis is preserved through finely regulated molecular mechanisms, some of them involving macromolecules called metabolic monitors. In particular, these systems control the cellular energy state by generating signaling molecules that counteract energy unbalancing through the stimulation of specific molecular targets. One of these metabolic monitors is adenylate kinase (AK). This enzyme coordinates different signaling pathways, ensuring adequate response to a broad range of functional, environmental and stress stimuli. In such a way, AK plays a key role in the cell and its dysfunction is connected to the onset of several diseases, such metabolic disorders, and cancer. 

It takes a fully setup metabolic network to supply the basic materials and literally an armada of complex enzymes to make adenosine monophosphate AMP, the starting point to make ATP, the energy molecule of the Cell. But it takes ATP along the whole process to make AMP, then Adenylate kinase to make ADP, and in the end, ATP synthase turbines to make ATP. What came first? The metabolic network? the nucleobases? The enzymes to make the nucleobases? ATP to supply energy to the enzymes to make AMP? This is truly a circle without a beginning and no end. A stepwise, gradual process based on prebiotic chemical evolution to produce all this described above is impossible. I think we are once again justified to say, life is an either all or nothing process. 

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Reduction - oxidation in molecular biology:  design or non-design ?

DNA (Deoxyribonucleic acid) is the core of life on Earth, every known living organism is using DNA to store information. 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 nucleus.  DNA is transcribed ( a copy of the " DNA message " into RNA (Ribonucleic acid ) is made. The machine doing this is RNA polymerase. When the RNA molecule is formed, it's further processed and carries its message out of the cell nucleus to the cytoplasm. Imagine a balloon filled with water, the water in the Cell is called cytoplasm, and further RNA travels to the Ribosome, that is the translation machine, where the information stored in digital form in the RNA molecule is translated, and what comes out is a sequence of amino acids which form a Protein molecule. The information that came from RNA has been translated and transformed now into analog form. This amino acid chain folds into a complex 3d structure which are proteins, the working horses inside the body of all living organisms.  

The structure of RNA nucleotides is very similar to that of DNA nucleotides, with the main difference being that the ribose sugar backbone in RNA has a hydroxyl (-OH) group that DNA does not. This gives DNA its name: DNA stands for deoxyribonucleic acid.

Enzymes/proteins need energy supply in order to work. Normally, in the form of ATP, or NADPH.

When a protein is " energized", that is, when it "charged", it is ready to perform work, in biochemistry terms, it is in a so-called  "reduced" state.  The requirement of transforming RNA's into DNA's is that the hydroxyl (-OH) group at position 2 on the pentose ribose sugar needs to be removed, and only a hydrogen atom remains. The removal is called " reduction " ( that's from where the enzyme has its name ) The name Hydroxyl comes from a combination of a Hydrogen atom with an Oxygen atom. In the reaction, the oxygen atom is separated and removed, and hydrogen remains. So RNA is deoxygenized, the oxygen atom is removed.
Now, ribonucleotide reductase, the protein which performs the reaction and removes the oxygen atom, gets changed in the process of that. It starts out in a reduced state and it ends up being oxidized. In the oxidized state, it means the energy has been consumed during the process, where the enzyme performed its reaction.  

We know when an enzyme changes it has to be changed back because if don’t change back, we get to a dead end where we have a dead enzyme and we can’t have that enzyme being dead because it’s necessary for making other deoxyribonucleotides. Well, it’s converted back to the reduced form by the action of a molecule called thioredoxin. Thio ( thio = sulfur groups. It stores its hydrogens in cysteine groups that form a sulfur bridge once oxidized )

Thioredoxin reduces or energetically "charges"  ribonucleotide reductase and in the process, it becomes oxidized by its own ( the energy is transferred from thioredoxin to RNR ). Well, you start thinking do we have to recycle that? The answer is yes. To replenish the thioredoxin in a reduced form, electrons are donated ultimately from any NADPH. They get to the thioredoxin by several steps, the thioredoxin is regenerated so that they can regenerate the ribonucleotide reductase.

Ribonucleotide reductase ( RNR) has 2 subunits, a large subunit and a small subunit.  The small subunit’s primary function is that it has a tyrosine amino acid within it that gets radicalized and that radicalization of the tyrosine is necessary for the reaction mechanism that produces the deoxyribonucleotides. RNR  controls the balance of all the deoxyribonucleotides and it does it with complex so-called allosteric controls. It’s a complicated process. The process starts with the tyrosyl radical in the small subunit of the ribonucleotide reductase. That radical actually pulls proton off of the ring of carbon 3' position on the ribose.  So tyrosine is pulling that hydrogen off and in the process of doing that it takes the electron with it leaving behind a radical, that’s on the ring. That creates some instability on the ribose and that instability on the ribose causes the hydroxyl position to pull a hydrogen off of the sulfhydryl of ribonucleotide reductase. You’ll notice that that creates a water molecule.

That H2O is lost, so the loss of the H2O results in now a ribose that has had the radical transferred to another position, that below that of position 2. Well, that radical is very much seeking a hydrogen, and we can see that that hydrogen is lost here from the other sulfur of the sulfhydryl on the ribonucleotide reductase to stabilize the overall sugar. At this point, we have now made the deoxyribose sugar. The radical has to be regenerated and that radical is regenerated by fixing the other part of the radical on the deoxyribose sugar that happens here, and as a result, the ribonucleotide reductase enzyme is completely regenerated into the radical state and simply has to be reduced by thioredoxin.

So, in order to get that cycle, you need Ribonucleotide reductase ( RNR), thioredoxin, thioredoxin reductase, and NADPH which comes from the pentose phosphate pathway.

This mechanism had to emerge PRIOR when life began. We can explain its origin either by natural unguided random processes, or design. Evolution depends on DNA, and DNA replication. So it does not explain the origin of any of the described enzymes and systems above.

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

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Peroxisome origins - another unsolved problem of an essential organelle

Researchers have long been puzzled as to how the cyanobacteria could make all that oxygen without poisoning themselves. To avoid their DNA getting wrecked by a hydroxyl radical that naturally occurs in the production of oxygen, the cyanobacteria would have had to evolve protective enzymes. But how could natural selection have led the cyanobacteria to evolve these enzymes if the need for them didn’t even exist yet? The explanations are fantasies at best.

Nick Lane describes the dilemma in the book Oxygen, the molecule that made the world:

Before cells could commit to oxygenic photosynthesis, they must have learned to deal with its toxic waste, or they would surely have been killed, as modern anaerobes are today. But how could they adapt to oxygen if they were not yet producing it? An oxygen holocaust, followed by the emergence of a new world order, is the obvious answer; but we have seen that there is no geological evidence to favor such a catastrophic history. In terms of the traditional account of life on our planet, the difficulty and investment required to split water and produce oxygen is a Darwinian paradox.

But thats the best part :

It was  suggested ‘that atmospheric hydrogen peroxide played a key role in inducing oxygenic photosynthesis because as peroxide increased in a local environment, organisms would not only be faced with a loss of reductant, but they would also be pressed to develop the biochemical apparatus (e.g., catalase) that would be ultimately be needed to protect against the products of oxygenic photosynthesis. This scenario allows for the early evolution of oxygen photosynthesis while global conditions were still anaerobic’

The role of the reactive oxygen species (ROS) family is that of a double-edged sword

while they act as secondary messengers in various key physiological phenomena, they also induce oxidative damages under several environmental stress conditions like salinity, drought, cold, heavy metals, UV irradiation etc., when the delicate balance between ROS production and elimination, necessary for normal cellular homeostasis, is disturbed.

How could evolution have evolved homeostasis of ROS ?????

http://reasonandscience.catsboard.com/t2645-peroxisome-origins-another-unsolved-problem-of-an-essential-organelle

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106 Re: My articles on Sat Jul 14, 2018 10:18 pm

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The alphabet, where does it come from ?
Atheist: Somebody created it
Hamlet?
Atheist: Shakespeare wrote it.
What about telecommunications, and information transmission systems?
Atheist: Engineers of big companies invented them
What about a Computer hard disk?
Atheist:  IBM engineers invented it, back in 1953
What about software?
Atheist: Software engineers invented them
What about Language Translation Systems and Digital Interpretation Headsets?
Atheist: People with skills of different languages made them.
The internet network ?
Atheist: Scientists developed it a few decades ago.

The Genetic Code , where does it come from?
Atheist: Science is working on it. We don't know yet
The information stored through the Genetic Code?
Atheist: Self-replicating RNA, then came DNA and random mutations and evolution through natural selection.
What about the information flow from the genome to transcription into messenger RNA, and decoding in the ribosome?
Atheist: Science hypothesizes chemical evolution, but is working on it...
What about the origin of DNA?
Atheist: Ah, there was the RNA world, and somehow ( science is working on it ) it was transformed into the DNA and protein world.  And then, evolution kicked in.
- very well.
What about the translation system in the Ribosome, from digital information stored in mRNA to amino acids and proteins? ( analog information? )
Atheist: Science is working on it, but it wasn't God.
What about intracellular signaling networks?
Atheist: They evolved by Darwinian evolution. No intelligent was required.

Very coherent and logical and rational. Makes perfect sense....

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107 Re: My articles on Sat Jul 14, 2018 10:50 pm

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Skeptos Style
Skeptos style
A warm happy atheist during the day
A classy skeptic who knows to defend unbelief  with a cup of coffee
An unbeliever whose heart warms when the night comes
Such a well versed atheist
He is the man
Such a man who is as smart as you in the daytime
One-shot shooter : luck and time. that's the deal
A man whose heart bursts when night comes
Such a man - smart things skepto thinks he has to say
Smart and well versed so he thinks he is
Yeah hey hey yeah you hey
So smart and eloquent
Yeah hey hey yeah you hey
I'm going to go from now on.
Skeptos Style
Skeptos Style O-O-O-Oh-Pan Skeptos Style
Skeptos Style O-O-O-Oh-Pan Skeptos Style
Well, sexy lady
Oh-oh-oh-oh-pan-jean style
Well, sexy lady
Oh-oh-oh-oh
Girl who looks quiet when she talks.... 
If you want to do know
Though it was covered, luck and time
is the deal, talks the woman
I am a man
I can see, time and luck
When the time comes,
A man who is more rugged than muscles
Such a man
Smart and brilliant
Yeah hey hey yeah you hey
Beautiful and lovely
Yeah hey hey yeah you hey
I will go from now on
Gangnam Style
Gangnam style oh-oh-oh-oh ...

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Quantum mechanics and Repair mechanisms in Ribonucleotide reductase enzymes point to intelligent design

Ribonucleotide reductases are some of the most challenging and complex enzymes I have encountered so far. And what I am discovering, is flabbergasting and mind-blowing. There are 3 different types. Class one uses a diiron-centered tyrosyl radical cofactor (Fe2–•Y122) that is essential for catalysis. In the E. coli reductase, the nucleotide substrate binds on the second subunit (R1) and while, presumably, Tyr on R2 is oxidized and reduced every time a nucleotide is reduced to a deoxynucleotide, the diiron(III) cluster of R2 remains unchanged. However, if a mistake occurs, and the diiron(III)–tyrosyl-radical Tyr is reduced by an exogenous small molecule, a repair system regenerates the tyrosyl radical cofactor.

So, 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 ( making DNA from RNA by removing an oxygen atom on the 2" of the ribose backbone), 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. It is a fundamental mechanism important in a wide range of biological processes including the universal reaction catalyzed by ribonucleotide reductases (RNRs) in making de novo, the building blocks required for DNA replication and repair.

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.

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. The enzyme and all these extremely precise reactions had to emerge prior when life began. The synthesis of the dii iron cluster is another story.

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 !!

RNR Mechanism and reaction
http://reasonandscience.catsboard.com/t2028-the-dna-double-helix-evidence-of-design#3435

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Biosynthesis of RNR cofactors, essential for life

Biosynthesis of RNR cofactors, essential for life

The synthesis of DNA molecules is essential for the Cell. The synthesis/make of the enzymes, Ribonucleotide reductases, that perform the reaction of transforming RNA molecules into DNA molecules is essential as well.

The system of energy generation and supply and recharging in order for the enzyme to perform its action must be fully set up.

DNA uses four different deoxyribonucleotide bases, and then the Cell must be able to produce the right overall amount depending on the stage of the Cell cycle, but also the right amount of each of the individual four bases.

A switch on the exterior of RNR's can either turn the enzyme on or off. All this is essential, otherwise the right amount would be not available for DNA replication, and a high mutation rate would be the consequence.

The RNR's reaction to remove the oxygen atom on the 2" position of the Ribose sugar base, and turn RNA into DNA, is depending on four sequential steps of high complexity.

The first reaction step depends on the existence and action of a highly complex metal cofactor,, by the abstraction of the hydrogen atom at the 3' position of the ribose moiety, which is a prerequisite for ribonucleotide reduction.

One very important set of modifications, often overlooked, is the assembly of metallocofactors essential for enzymatic activity.

The Cell needs to synthesize this cofactor. Fe-S protein–diflavin reductase complex, Dre2–Tah18, another molecular machine, plays a critical role in RNR cofactor biosynthesis.

Cells with diminishing Dre2 have significantly reduced ability to make deoxynucleotides (DNA).

In response to DNA damage, an activated checkpoint kinase cascade increases RNR production levels.

An additional layer of RNR regulation is directly correlated with nucleotide reduction activity, involves the assembly and maintenance of this essential cluster.

An estimated one-third of proteins require metals for their function. Recent studies have established the importance or essentiality of biosynthetic pathways for cluster insertion and have suggested the importance of repair or maintenance pathways for regenerating active cofactors from damaged metal clusters.

A number of generalizations are emerging concerning nature’s design and implementation of metallocofactor biogenesis.

Nature, or the designers design?

The cofactors of many metalloproteins are generated by defined biosynthetic pathways. ( How were theses pathways defined ? )

Metals are transferred in their reduced state to facilitate ligand exchange between protein factors.

Specific protein factors include a metal insertase or chaperone to deliver the metal, specific redox proteins such as flavodoxins or ferredoxins that control the oxidation state of the metal, and GTPases or ATPases involved in protein unfolding/refolding to allow metal entrance into deeply buried active sites. ( Metal insertases can be viewed as protein machines used to make parts used in other molecular machines, which are required to make the basic building blocks of life )

There is often biological redundancy in pathway factors (e.g., multiple ferredoxins) ( Which promotes robustness and diminishes synthesis mistakes. Could nonguided random mechanisms explain this feat ? )

There is a hierarchy of metal delivery to proteins. ( How was this hierarchy established ? )

Compartmentalization (e.g., periplasm versus cytosol in prokaryotes) and relative affinities of protein coordination environments for various metals in relation to the intracellular concentrations of those metals contribute to prevention of mismetallation. ( How did this coordination emerge ? )

Metal clusters can become damaged by oxidants such as NO and O2•−, and specific pathways are implicated in their repair. ( How did these repair mechanisms emerge prebiotically ? )

All described above is an abiogenesis problem - no evolutionary mechanisms explain the origin of metal cluster biosynthesis required in RNR's, essential for DNA synthesis.

More: RNR Mechanism and reaction
http://reasonandscience.catsboard.com/t2028-the-dna-double-helix-evidence-of-design#3435



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