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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110 Re: My articles on Sun Jul 22, 2018 6:15 am

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The biochemical - molecular world is full of unexplored surprising landscapes.

And the discovery of them is exciting and rewarding to anyone that makes the effort to learn and understand what is going on inside living cells. When I investigate something, my modo-operandi is to play Sherlock Holmes. I ask about how something came to be, then dig deeper and deeper until I reach the bottom. And there, not rarely, hidden awe-inspiring treasures and unimagined complexity awaits. Its Gods playground, where he reveals how he employed his brilliant unfathomable and incredible intelligence when he made life

The make of all building blocks of life depend and are branched and interconnected to the trunk-like central metabolic pathways, that is the pentose phosphate pathway, glycolysis, and the Citric acid cycle.

There would be no life without these central production factories, and the elucidation of how they emerged is fundamental to understand and provide possible explanations of the origin of life. Whenever i research the biosynthesis of a molecule, somehow these central pathways play a role, and are required. 

Following paper:

Origin and evolution of metabolic pathways begins with following sentence:

The emergence and evolution of metabolic pathways represented a crucial step in molecular and cellular evolution.

My comment: It is deceptive to portray this issue as a problem of evolution. Why shift the focus to evolution, if there was no evolution prior when life began? Simple. Because there is no other "plausible" mechanism. If the authors had to admit the real situation, they would have to mention random, unguided, lucky, self-organization based on chaotic chemical reactions without a guiding hand. But portray the alternative to intelligent design as what it truly is, that would de-mascarade it what it is:  unbelievable and irrational. To avoid the truth, science based on methodological naturalism hides behind evolution, which is always acceptable and sounds sciency, and inspires trust and seriousness. 

But for a critical and unbiased investigator and observer, the situation is different. On the molecular level, the unfathomable intelligence of the Creator shines through all over, like an unavoidable, shining light.

The beforementioned paper continues:
" In fact, the exhaustion of the prebiotic supply of amino acids and other compounds that were likely present in the ancestral environment, imposed an important selective pressure, favoring those primordial heterotrophic cells which became capable of synthesizing those molecules.".

That portrays a situation where amino acids were abundant on early earth, screaming and hand-waving to Saint Luck: " Here we are !! Select us, i want to be incorporated into proteins !! ". We want to become complex machines !! Yah sure....

Some, even today, when questioned about the origin of life, claim that the Miller experiment solved the issue in regard of the origin of life. Well, yeah!! Not exactly. Besides the fact, that even IF Miller's experiment would prove that the 20 canonical amino acids necessary for life could have been ready available on early earth, that would far from prove that life from nonlife, randomly, is possible. 

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.

These building blocks would exist and have to compete with at least 500 other Amino Acids to be selected, and then, in a sufficient amount. They would have had to be selected amongst all others, and their handedness as well. ( They had to be all 100% left-handed, a mix of lefthanded and righthanded AA's doesn't work ). In Millers 1952 experiment, only a small fraction of racemic AA's were synthesized, and even in the subsequent experiments performed in 2008, and 2010, many essential AA's were not made available.

The Miller Urey experiment
http://reasonandscience.catsboard.com/t2170-the-miller-urey-experiment#5388

If you can't make a brick, you can't make a house. Naturalistic scenarios are all based on ad-hoc anecdotal pseudo-scientific claims.
Without having the right twenty left-handed amino acids,  life essential proteins cannot be made, nor protein complexes, nor biological cells.

But the awe inspiring point comes as follows: Never, in any simulated OOL experiment, the amino acid Tryptophan was synthesized. Why? The biosynthesis pathway to make tryptophan is the most biochemically expensive and most complicated process of all life essential amino acid pathways, and tightly regulated. Glucose feeds the Glycolysis pathway, which utilizes nine enzimatic steps and enzymes to produce phosphoenolpyruvate (PEP) and erythrose- 4-phosphate, which enter the Shikimake pathway, which uses another seven enzymes, to make chorismate, which enters the Tryptophan biosynthesis pathway , and after another five steps and enzymes, finally produces Tryptophan. So, in total, 21 enzymes. 


But not any kind of enzyme. Some are highly sophisticated, veritable multienzyme nanomachines, like a paper called the bacterial tryptophan synthase, which channels the substrates through a long interconnecting tunnel with a clear logic: the substrate  is not lost from the enzyme complex and diluted in the surrounding milieu. This phenomenon of direct transfer of enzyme-bound metabolic intermediates, or tunneling, increases the efficiency of the overall pathway by preventing loss and dilution of the intermediate. Smart, hah ??!!

You can have a closer look at the entire pathway to make tryptophan here:
http://reasonandscience.catsboard.com/t1740-origin-of-the-canonical-twenty-amino-acids-required-for-life#5939

Now let me tell you why this is so relevant. Tryptophan is the substrate, used to make one of the most important electron carriers used in life: NAD:

Nicotinamide adenine dinucleotide (NAD) in origin of life scenarios
http://reasonandscience.catsboard.com/t2708-nicotinamide-adenine-dinucleotide-nad-in-origin-of-life-scenarios#6060

NAD is pivotal for cell life, first as a reusable redox coenzyme for energy production, second as a consumable substrate in enzymatic reactions regulating crucial biological processes, including gene expression, DNA repair, cell death and lifespan, calcium signaling, glucose homeostasis, and circadian rhythms.  (NADPH) is an essential electron donor in all organisms. It provides the reducing power that drives numerous anabolic reactions, including those responsible for the biosynthesis of all major cell components. It is also the driving force of most biosynthetic enzymatic reactions, including those responsible for the biosynthesis of all major cell components, such as DNA and lipids. The consumption of NADP+ is connected to the consumption of NAD+ and to the regulation of various major biological activities such as DNA repair, gene expression, apoptosis, nitrogen fixation, and calcium homeostasis.  (NADPH) is an essential electron donor in all organisms. It provides the reducing power that drives numerous anabolic reactions, including those responsible for the biosynthesis of all major cell components.


I'd like to see what Darwin would comment on that. What do you ??!! Still struggle to let chance go ??!!

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111 Re: My articles on Mon Jul 23, 2018 6:21 am

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The molecular world is full of unexplored surprising landscapes

And the discovery of them is exciting and rewarding to anyone that makes the effort to learn and understand what is going on inside living cells. When I investigate something, my modo-operandi is to play Sherlock Holmes. I ask about how something works, and what is required to make it work, and how it might have come to be, then dig deeper and deeper until I reach the bottom. And there, not rarely, hidden awe-inspiring treasures and unimagined complexity, interdependence, and relationships awaits. Its Gods playground, where he reveals how he employed his brilliant unfathomable and incredible intelligence when he made and created life.

The make of all building blocks of life depend and are branched and interconnected to the trunk-like central metabolic pathways, that is the pentose phosphate pathway, glycolysis, and the Citric acid cycle.

There would be no life without these central production factories, and the elucidation of how they emerged is fundamental to understand and provide possible explanations of the origin of life. Whenever i research the biosynthesis of a molecule, somehow these central pathways play a role, and are required. Of course, science is clueless, but the most various " hypotheses " and " wannabe scenarios " abound.

Following paper:

" Origin and evolution of metabolic pathways "  begins with following sentence:

The emergence and evolution of metabolic pathways represented a crucial step in molecular and cellular evolution.

My comment: It is deceptive to portray the origin of the central metabolic pathways as a problem of evolution. Its not.  Why shift the focus to evolution, if there was no evolution prior when life began? Simple. Because there is no other "plausible" naturalistic mechanism. If the authors had to admit the real situation, they would have to mention random, unguided, lucky, self-organization based on chaotic chemical reactions without a guiding hand. But portray the alternative to intelligent design as what it truly is, that would de-mascarade it to what it evidently comes to be:  unbelievable and irrational. To avoid however that truth, science based on methodological naturalism hides behind evolution, where enough efforts have been spent to make it always acceptable to the crowd, and it sounds sciency,  and meant to inspire trust and seriousness.

But for a critical and unbiased investigator and observer, the situation is different. On the molecular level, the unfathomable intelligence of the Creator shines through all over, like an unavoidable, shining light.

The beforementioned paper continues:
" In fact, the exhaustion of the prebiotic supply of amino acids and other compounds that were likely present in the ancestral environment, imposed an important selective pressure, favoring those primordial heterotrophic cells which became capable of synthesizing those molecules.".

That portrays a situation where amino acids were abundant on early earth, screaming and hand-waving to Saint Luck: " Here we are !! Select us, i want to be incorporated into proteins !! ". We want to become complex machines !! Yah sure....

Some, even today, when questioned about the origin of life, claim that the Miller experiment solved the issue in regard of the origin of life. Well, yeah!! Not exactly. Besides the fact, that even IF Miller's experiment would prove that the 20 canonical amino acids necessary for life could have been readily available on early earth, that would far from prove that life from nonlife, randomly, is possible.

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.

These building blocks would exist and have to compete with at least 500 other Amino Acids to be selected, and then, in a sufficient amount. They would have had to be selected amongst all others, and their handedness as well. ( They had to be all 100% left-handed, a mix of lefthanded and righthanded AA's doesn't work ). In Millers 1952 experiment, only a small fraction of racemic AA's were synthesized, and even in the subsequent experiments performed in 2008, and 2010, many essential AA's were not made available.

The Miller Urey experiment
http://reasonandscience.catsboard.com/t2170-the-miller-urey-experiment#5388

If you can't make a brick, you can't make a house. Naturalistic scenarios are all based on ad-hoc anecdotal pseudo-scientific claims.
Without having the right twenty left-handed amino acids,  life essential proteins cannot be made, nor protein complexes, nor biological cells.

But the awe-inspiring point comes as follows: Never, in any simulated OOL experiment, the amino acid Tryptophan was synthesized. Why? The biosynthesis pathway to make tryptophan is the most biochemically expensive and most complicated process of all life essential amino acid pathways, and tightly regulated. Glucose feeds the Glycolysis pathway, which utilizes nine enzymatic steps and enzymes to produce phosphoenolpyruvate (PEP) and erythrose- 4-phosphate, which enter the Shikimake pathway, which uses another seven enzymes, to make chorismate, which enters the Tryptophan biosynthesis pathway, and after another five steps and enzymes, finally produces Tryptophan. So, in total, 21 enzymes.

But not any kind of enzyme. Some are highly sophisticated, veritable multienzyme nanomachines, like a paper called the bacterial tryptophan synthase, which channels the substrates through a long interconnecting tunnel with a clear logic: the substrate is not lost from the enzyme complex and diluted in the surrounding milieu. This phenomenon of direct transfer of enzyme-bound metabolic intermediates, or tunneling, increases the efficiency of the overall pathway by preventing loss and dilution of the intermediate. Smart, hah ??!!

You can have a closer look at the entire pathway to make tryptophan here:
http://reasonandscience.catsboard.com/t1740-origin-of-the-canonical-twenty-amino-acids-required-for-life#5939

Now let me tell you why this is so relevant. Tryptophan is the substrate, used to make one of the most important electron carriers used in life: NAD:

Nicotinamide adenine dinucleotide (NAD) in origin of life scenarios
http://reasonandscience.catsboard.com/t2708-nicotinamide-adenine-dinucleotide-nad-in-origin-of-life-scenarios#6060

NAD is pivotal for cell life, first as a reusable redox coenzyme for energy production, second as a consumable substrate in enzymatic reactions regulating crucial biological processes, including gene expression, DNA repair, cell death and lifespan, calcium signaling, glucose homeostasis, and circadian rhythms.  (NADPH) is an essential electron donor in all organisms. It provides the reducing power that drives numerous anabolic reactions, including those responsible for the biosynthesis of all major cell components. It is also the driving force of most biosynthetic enzymatic reactions, including those responsible for the biosynthesis of all major cell components, such as DNA and lipids. The consumption of NADP+ is connected to the consumption of NAD+ and to the regulation of various major biological activities such as DNA repair, gene expression, apoptosis, nitrogen fixation, and calcium homeostasis.  (NADPH) is an essential electron donor in all organisms. It provides the reducing power that drives numerous anabolic reactions, including those responsible for the biosynthesis of all major cell components.

I'd like to see what Darwin would comment on that. What do you ??!! Still struggle to let chance go ??!!



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112 Re: My articles on Mon Jul 23, 2018 11:09 pm

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Three different Co-factors in Ribonucleotide reductase enzymes point to design

Ribonucleotide reductase does not only belong to one of the most essential and fundamental enzymes in life, which are the only ones producing deoxyribonucleotides, or in short, DNA, but are also one of the most complex ones.

Ribonucleotide reductases, (RNR's), are a major problem for evolutionary scenarios. Not only because they had to emerge prior when life began, but because there are three diverging classes and three subclasses. They have the same catalytic activity, but different amino acid sequences. Only traces of evidence for homology remain in the sequences themselves. These motifs are inadequate to provide a statistically significant case for homology. To claim common ancestry, in this case, is an ad-hoc assertion. Truth said, science is unable to infer a reasonable scenario of divergence starting from a common ancestor, a protoRNR, and all it can do, is resort to made-up stories. The striking thing is, that RNR's use, all three classes, the same allosteric binding mechanism to regulate the needed amount of each of the four deoxynucleotides required by the cell. BUT, they use radically different co-factors which are essential for the four-step reaction to occur. And that is a major problem for naturalistic proposals.  

Class I RNR's use a diiron-centered tyrosyl radical cofactor that is essential for catalysis. It promotes a long distance radical transfer to the reaction site from one subunit to the other.
Class II uses a coenzyme Vitamin B12 ( AdoCbl ). Vitamin B12 is exceptional in comparison to other vitamins and coenzymes for several reasons. Firstly, there is its structural complexity, which is also reflected in its biosynthetic requirements such that somewhere around thirty genes and nearly 30 enzymatic steps in one of nature’s largest characterized biosynthetic pathways are required and necessary for its complete de novo synthesis. Secondly, B12 is unique amongst the vitamins in that its synthesis is restricted to certain microorganisms.

Class III use an Iron-sulfur cluster as cofactor, which is generated by defined biosynthetic pathways, in a joint venture with S-adenosylmethionine (SAM), which is a conjugate of nucleotide adenosine and amino acid methionine, two ubiquitous biological compounds. The three co-factors have nothing in common but perform the same function.  

One science paper made the attempt to explain its origin as follows:

"Assuming an evolutionary process based on tinkering, i.e., modification of present components rather than inventions from scratch, our model tries to deviate as little as possible from what is observed in modern biochemistry."

Amazing. An evolutionary process based on tinkering. Let that sink in for a moment.... How does such a proposal make sense? If the author wishes not to deviate much from the mechanisms observed in modern enzymes, he would have to explain the origin of the most complex biosynthesis pathways to produce one of the most sophisticated cofactors known ( Vitamin B12 in RNR Class II enzymes ), and why nature "invented" two other, radically different co-factors for the same reaction, while keeping another mechanism, namely allosteric regulation, identical in all three classes.  That is not logical nor rational. An evident answer would be that intelligence with specific goals was involved, namely to create the most effective and advanced bio-informational molecule known to man: DNA, but by separate enzymatic routes, for reasons, that only God knows.

Science is clueless in such a degree, that another source made a 100% opposite claim to the before mentioned one:

Iron-Sulfur Clusters in Chemistry and Biology, page 258:
The conversion of ribonucleotides into deoxyribonucleotides is catalyzed by three evolutionarily unrelated ribonucleotide reductases (RNR).

Ha!! How funny is that ??

So the same result is achieved by using the same allosteric binding mechanism for regulation, but three completely different co-factors - for no apparent reason. To make things even more perplexing: Some of the reactions are strictly anaerobic, while others require molecular oxygen. And some bacteria use more than one type of RNR's. A true tohuwabohu. And, last not least. These co-factors are essential for the enzyme reaction. If one goes havoc, there are sophisticated repair mechanisms - for each, for every one of them, tailored to each of them !! For every of the three co-factors, there are specific regulation, regeneration, and repair mechanisms inbuilt. No teleology involved ? I doubt so.  

The answer that science can come up with, is to make up scenarios and hypotheses, which, however, in the end, leave much doubt. The explanations are guesswork and ad-hoc assertions which bear no relevance to reality. Design is by far a more compelling explanation.

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

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113 The catacombes of the Christians on Wed Jul 25, 2018 4:27 pm

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If you have the opportunity to visit Rome, i recommend that you visit the Catacombes of the Christians. I have done it, and it was an amazing experience. They extend for kilometers under the earth, and hundreds of thousands of Christians were buried there. When you see the frescos and depictions of the apostles Paul and Peter, you feel very near to what the Bible tells and relates about them.

The catacombs we visited were named of Saint Domitilla,
http://www.domitilla.info/idx.htm?var1=docs/en00.htm

where Saint Petronilla was buried, which was supposed to be St. Peters dautghter:
https://en.wikipedia.org/wiki/Saint_Petronilla

Its amazing, a very touching experience.

'Oldest' image of St Paul discovered

http://www.telegraph.co.uk/news/worldnews/europe/vaticancityandholysee/5675461/Oldest-image-of-St-Paul-discovered.html

28 Jun 2009
The fresco, which dates back to the 4th Century AD, was discovered during restoration work at the Catacomb of Saint Thekla but was kept secret for ten days.

During that time experts carefully removed centuries of grime from the fresco with a laser, before the news was officially announced through the Vatican's official newspaper L'Osservatore Romano.

There are more than 40 known Catacombs or underground Christian burial places across Rome and because of their religious significance the Vatican's Pontifical Commission of Sacred Archeology has jurisdiction over them.

A photograph of the icon shows the thin face of a bearded man with large eyes, sunken nose and face on a red background surrounded with a yellow circle – the classic image of St Paul.

The image was found in the Catacomb of St Thekla, close to the Basilica of St Paul Outside the Walls in Rome, which is said to be built on the site where he was buried.

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Why do cells go to the trouble of methylating uracil to thymine before it can be used in DNA?

During nucleotide synthesis,  ribonucleotides that form RNA, are transformed into deoxyribonucleotides that form DNA by Ribonucleotide reductase enzymes. Before being incorporated into the chromosomes, another essential modification takes place. Uracil bases in RNA are transformed into thymine bases used in DNA. There is a life essential requirement, why.

Cytosine, the second of the two pyrimidine bases used in DNA, do deaminate over time into uracil bases. If uracil would remain, and not be replaced by thymine in DNA,  it would mix with the cytosine which deaminated spontaneously into uracil -  occurring on average, 100 times per day in the cell. If there wasn't a mechanism to remove the deaminated nucleotides ( deoxyuridine triphosphate - dUTP's ), then, gradually over time, all of the Cytosine-Adenine base pairs would become Uracil-Adenine base pairs.

If uracil would be transformed from RNA to DNA, transforming it into deoxy uracil, and used in DNA like it is in RNA, and not replaced with thymine, then it would keep being recognized as deaminated cytidine by the repair machinery, and removed as well,  and the DNA would be basically coated in uracil DNA glycosylases repair enzymes removing the deaminated base pairs, together with the legitimate ones. So, instead, DNA uses thymidine, which is distinguishable biochemically from uracil by its extra methyl group. This way the cell gains the essential ability to remove the uracils that are a result of deamination using uracil DNA glycosylase enzymes, preventing mass mutation in its genome without removing the thymine base that it actually needs to be there.

The buildup of these “illegitimate” uracils could be catastrophic for the organism - at the very least, copying fidelity of DNA would be detrimentally affected. Thus, cells have repair systems in place to remove these “illegitimate” uracils. But if uracil were already present in DNA, paired to adenine, the repair system would be forced to somehow differentiate between “illegitimate” and “legitimate” uracils. An easy solution to this problem? Add a methyl group to all of the “legitimate” uracils, allowing the repair system to easily tell between the two. This usage of methylated uracil, or thymine, in DNA allowed for the long-term storage of crucial genetic information.

But why would prebiotic molecules without distant goals nor purpose to produce a stable information storage medium, DNA, promote this base exchange, and produce error check and repair mechanisms to keep the information intact and promote high-fidelity replication and maintain the mutation levels low?

Only one extra synthetic step in nucleotide biosynthesis is required to achieve the exchange of uracil to thymine, but the machinery to do the job is enormously complex.

After further phosphorylation, that is, adding two phosphate groups to the deoxynucleotide monophosphates, they become deoxynucleotide triphosphates dGTP, dATP, dCTP, and dTTP and can be used as the building blocks to construct DNA.

The deoxynucleotide triphosphates (dNTPs) are the building blocks for DNA replication (they lose two of the phosphate groups in the process of incorporation and polymerization).   Phosphorylation status of nucleotides is regulated by NDP kinases and NMP kinases that use ATP pool as their cross-phosphorylation source.

Methylation protects the DNA. Beside using thymine instead of uracil, most organisms also use various enzymes to modify DNA after it has been synthesized. Two such enzymes, dam and dcm methylate adenines and cytosines, respectively, along the entire DNA strand. This methylation makes the DNA unrecognizable to many Nucleases (enzymes which break down DNA and RNA), so that it cannot be easily attacked by invaders, like viruses or certain bacteria. Obviously, methylating the nucleotides before they are incorporated ensures that the entire strand of DNA is protected.

Thymine also protects the DNA in another way. If you look at the components of nucleic acids, phosphates, sugars, and bases, you see that they are all very hydrophilic (water soluble). Obviously, adding a hydrophobic (water-insoluble) methyl group to part of the DNA is going to change the characteristics of the molecule. The major effect is that the methyl group will be repelled by the rest of the DNA, moving it to a fixed position in the major groove of the helix. This solves an important problem with uracil - though it prefers adenine, uracil can base-pair with almost any other base, including itself, depending on how it situates itself in the helix. By tacking it down to a single conformation, the methyl group restricts uracil (thymine) to pairing only with adenine. This greatly improves the efficiency of DNA replication, by reducing the rate of mismatches, and thus mutations.

To sum up: the replacement of thymine for uracil in DNA protects the DNA from attack and maintains the fidelity of DNA replication.

Above relates to the question how a prebiotic environment could have been able to come up and emerge with this elaborate information storage system, and error check and repair machines, essential to keep the integrity of the DNA molecule.
There was no evolution yet.

So what does explain its origin best? Spontaneous self-assembly by orderly molecular aggregation of the building blocks in a sequentially correct manner without external direction, or design?

More:
http://reasonandscience.catsboard.com/t2028-the-dna-double-helix-evidence-of-design#3519

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

The pastors of atheism have finally written the bible of scientific atheism, now it is left to their faithful devotees to spread the good news:
"Zero energy, the nothing that is the minimal state of energy produces wonders, even universes."
" Life is the feat of prebiotic chemistry shake n'shake in, which self-assembled spontaneously by orderly aggregation and sequentially correct manner without external direction to create the most advanced miniature factory of the universe "
Word of salvation, let us pray, brothers



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

It's very very likely, or maybe better, extremely likely, that an intelligent creator - God exists. Its so likely, that we are justified to be absolutely confident and sure about that - God deserves to be believed. And many lines of evidence - historical, archeological, theological, logical, rational, mathematical, observational, philosophical, scientific reasons permit to infer that it's most probably the Judeo-Christian God that revealed himself first as Jahwe, in the Old Testament, and as Jesus Christ from Nazareth, in the New Testament. Blessed, who believes.

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

The Religion someone holds on to is a secondary issue

The right approach to find truth in regards to origins, and endorse a worldview that makes sense, is a consequence of a carefully chosen and elaborated methodology of an epistemological framework, and applied to do a consistent, correct to the case research, and coming to meaningful, and the most accurate possible conclusions in regards of origins and reality. There are several ways, as rationalism, empiricism, pragmatism, authority, and revelation.

Rationalism holds that which is logical and consistent is true.

Empiricism holds that what can be systematically verified via sensory input is the way to accept the truth.

Pragmatism bases and derives its claims via practical life experience.

Authority is based on what experts say is true. And

revelation holds that which God reveals is True; Revelations from God establish Truth.

A correct research to find truth is based on considering a mix of above. Atheists do commonly make the mistake to stick to empiricism and authority only. But someone has to consider the aspects of science, philosophy, theology, and applying reason, wisdom, and logic.

Agnosticism should be the starting point, and Christ ( in my experience ) is the best conclusion and the end station of the journey, and the answer which will provide peace of spirit, intellect, and the mind. And beginning to live with HIM, and IN HIM, is a new starting point of a spiritual awakening, and a new journey, based on peace with God, confidence, and faith in him, accepting a new direction in life, based on the Lord's guidance and will. The end station will be eternal joy in his presence. Hope you are in... and on the right way.



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115 A nightmare of an enzyme on Mon Jul 30, 2018 9:55 pm

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A nightmare of an enzyme for naturalistic proposals

http://reasonandscience.catsboard.com/t2028-the-dna-double-helix-evidence-of-design#3519

In Catholic parlance, the devil runs from holy water.  Similarly, Darwin would probably turn around in his grave, if he knew about Thymidylate Synthase enzymes and the implications for his ideas. This is truly a nightmare of an enzyme for proponents of evolution. First of all, it belongs to life-essential enzymes. It can safely be said, there would be no life, of any form, without the reaction it performs. Koonin calls Thymidylate synthase a strictly essential enzyme of DNA precursor biosynthesis. DNA depends on it, therefore, it had to be there prior evolution could kick in.  

The transition from RNA to DNA according to the evolutionary narrative, goes in two steps. First, Ribonucleotides ( RNA ) are transformed into Deoxyribonucleotides ( DNA ) through Ribonucleotide reductase enzymes. Secondly, Uracil is the RNA base and must be transformed into its equivalent, Thymine, in DNA.


"Thymidylate synthase enzymes are essential for all DNA-based forms of life and therefore implicated in the hypothesized transition from RNA to DNA genomes."  Thymidylate synthetase (TS) enzymes catalyze the conversion of deoxyuridine monophosphate (dUMP)  into deoxythymidine monophosphate (dTMP).

Here is the amazing logic, why: If uracil would be transformed from RNA to DNA, transforming it into deoxy uracil, and used in DNA like it is in RNA, and not replaced with thymine, then it could keep being recognized as deaminated cytidine by the repair machinery, and removed as well,  and the DNA would be basically coated in uracil DNA glycosylases repair enzymes removing the deaminated base pairs, and the legitimate ones. So, instead, DNA uses thymidine, which is distinguishable biochemically from uracil by its extra methyl group. This way the cell gains the essential ability to remove the uracils that are a result of deamination using uracil DNA glycosylase enzymes, preventing mass mutation in its genome without removing the thymine base that it actually needs to be there.

Defects in the Thymidylate Synthase enzymes activity cause various biological and genetic abnormalities, such as thymineless death. Thymidylate synthase (TS) plays a crucial role in the early stages of DNA biosynthesis, and insertion of healthy DNA is vital for normal body functions and avoidance of cancerous activity.

Its remarkable that for several decades only one chemical pathway was known for the de novo biosynthesis of the essential DNA nucleotide, thymidylate. BUT: Thymidine is unique to DNA can be synthesized by two radically
different enzymes that have NO similarity in sequence or structure.  Recently a family of thymidylate synthases (ThyXs) was identified.

The residues essential for catalysis in ThyA are absent in ThyX proteins. 10 Multiple studies have identified key differences in the molecular mechanism of catalysis between flavin dependent TSs ( FDTS's) and classic TSases.

My comment: Wow !! This is extraordinary. An enzyme, that has no homology, that is, no shared ancestry, and had to emerge prior when life began, that means the prebiotic convergent emergence of an enzyme with the same function and reaction, but it emerged twice by different routes.  That should be perplexing for any advocate of naturalistic explanations.

The authors continue: "Although deoxythymidylate cannot be provided directly by ribonucleotide reductase, the gene encoding thymidylate synthase ThyA is absent from the genomes of a large number of nonsymbiotic microbes. We show that ThyX  proteins of previously unknown function form a large and distinct class of thymidylate synthases. ThyX has a wide but sporadic phylogenetic distribution, almost exclusively limited to microbial genomes lacking thyA. ThyX and ThyA use different reductive mechanisms because ThyX activity is dependent on reduced flavin nucleotides. The mechanism of the FDTS-catalyzed reaction differs greatly from that of the classical thymidylate synthases. "
" thyX and thyA genes have mutually exclusive phylogenetic patterns. thyX can functionally replace thyA in dTMP synthesis. "

My comment:  This is an enzyme, that had to emerge prior when self-replication of life began, that by two non-homologous routes catalyzes the same reaction. And these two diverging routes are truly complex, involving four distinct synthesis steps, and other enzymes for redox reactions and energy supply. 

Evolution of Thymidylate Synthase
In the paper: An Evolutionary Analysis of Lateral Gene Transfer in Thymidylate Synthase Enzymes, the authors write as follows:
Thymidylate synthases are essential for all DNA-based forms of life and therefore implicated in the hypothesized transition from RNA genomes to DNA genomes. Two evolutionally unrelated Thy enzymes, ThyA and ThyX, are known to catalyze the same biochemical reaction. For decades, only one family of thymidylate synthase enzymes was known, and its presence was considered necessary to maintain all DNA-based forms of life. Then, a gene encoding an alternative enzyme was discovered and characterized. The novel enzyme was named ThyX, whereas the other enzyme was renamed ThyA. The 2 enzymes, ThyA and ThyX, were found to have distinctly different sequences and structures, thus alluding to independent evolutionary origins.

Most, if not all scientific papers, do not make a distinction between life essential parts that had to emerge prior life started, and other parts that came afterward. A clear distinction should be made what can be explained by biological evolution, and what cannot. Thymidylate Synthase is claimed to be necessary in a transition state from the so-called RNA to the DNA world. The article: Ancient enzymes reveal the DNA genesis says as follows: " Nature made at least three new types of inventions in assembling living cells from building blocks produced by prebiotic chemistry", and continues: " heritable blueprints – genetic coding –furnished sufficient continuity for complexity to grow. The most dramatic of these inventions were all completed and probably overwritten before the first living cells appeared.  So, DNA is clearly a pre-life invention. And cannot be explained by Darwinian evolution.

By virtue of their function and phyletic distribution, Thys are ancient enzymes, implying 1) the likely participation of one or both enzymes during the transition from an RNA world to a DNA world (based on protein catalysts: and 2) the probable presence of a gene encoding Thy in the genome of the common ancestors of eukaryotes, bacteria, and archaea.

This claim is even more noteworthy. The authors suggest a pre-existing gene encoding these enzymes. How could that be, if the enzyme is responsible to produce thymidylate triphosphate (dTTP), one of the four nucleotides that constitute DNA? - and therefore, genes were not existing yet? This is one of the many classic chicken-egg situations, which are encountered all over in biological Cells. 

"The evolutionary phenomenon whereby the same archaeon or bacterium encodes 2 structurally distinct enzymes performing the same function is postulated to be a possible transition stage in lateral gene transfer (LGT) and subsequent gene loss".

This is an ad-hoc claim. The authors do not question, why a prebiotic, pre-life mechanism, be it chemical evolution, self-assembly, physical laws or mere chance would have come up with two distinct complex mechanisms, performing the same reaction. These questions would not find a satisfying answer based on naturalism. So wipe them under the table and not asking, is more comfortable. But that does not put them away. There is no way these enzymes could have emerged prebiotically, by mere naturalistic means, and then, the authors make up another just so scenario: The two routes are explained by lateral gene transfer. No more, no less. This is nothing more than inventing stories. It has nothing to do with science and makes no sense whatsoever.

But there is more. How could lateral gene transfer explain the makeup of the second enzyme, if it is not homologous?  - that is if the amino acid sequence is largely different? This seems to me an explanation out of despair. The authors could not imagine anything else, and came up with this story.... I don't buy it. Do you ??!!






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116 Re: My articles on Sat Aug 04, 2018 10:23 am

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Atheists commonly confess ignorance and base it on the claim that there is no evidence of God. The consequence of such a position is:

the lack of
objective moral values
meaning of life
lack of recognition of the real intrinsic value of human beings
what really matters in life ( to love God, and your next )
hope
understanding
inner peace
knowledge
security

and become a playball of their own

desires
wishes
will
inclinations
insecurity
hopelessness
meaninglessness
lacks values
certainty of anything
decisions
egoism
greed
lack of goals in life
frustration
bad decisions
lack of direction in life
the consequences are:
Increase of crimes
homicides
abortions
suicide
betrayals
robbery
separations
destructuration of families
telling lies
envy

false doctrines and various isms which undermine the value of life, like
nazism
communism

and the ultimate fate and consequence is

to die and be judged upon their own sins and mistakes and paying for their sins and rejection of God in Hell forever and ever.



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Naturalism is like alchemy

The philosophical and proto-scientific attempt of alchemy in the middle age has never succeeded. Whether it is chrysopoeia,  panacea, nor alkahest, magnum opus brought only one result, attempt after attempt: failure. Naturalists seem not to have learned from the middle ages, with the hope to make the impossible to become possible.

In the same sense as copper, plastic, basic electronic components do not turn into a  printed circuit board randomly, genes, proteins, and metabolites do not turn into a metabolic network by unguided processes.

How Cellular Enzymatic and Metabolic networks  point to design

http://reasonandscience.catsboard.com/t2371-how-cellular-enzymatic-and-metabolic-networks-point-to-design

The argument of an intelligent designer required to set up the Metabolic Networks for the origin of life

Observation: The existence of metabolic pathways is crucial for molecular and cellular function.  Although bacterial genomes differ vastly in their sizes and gene repertoires, no matter how small, they must contain all the information to allow the cell to perform many essential (housekeeping) functions that give the cell the ability to maintain metabolic homeostasis, reproduce, and evolve, the three main properties of living cells. Gil et al. (2004)  In fact, metabolism is one of the most conserved cellular processes. By integrating data from comparative genomics and large-scale deletion studies, the paper "Structural analyses of a hypothetical minimal metabolism"   proposes a minimal gene set comprising 206 protein-coding genes for a hypothetical minimal cell. The paper lists 50 enzymes/proteins required to create a metabolic network implemented by a hypothetical minimal genome for the hypothetical minimal cell. The  50 enzymes/ proteins, and the metabolic network must be fully implemented to permit a cell to keep its basic functions.
 
Hypothesis (Prediction): The origin of biological irreducible metabolic pathways which also require regulation and which are structured like a cascade, similar to electronic circuit boards,  are best explained by the creative action of an intelligent agent.

Experiment: Experimental investigations of metabolic networks indicate that they are full of nodes with enzymes/proteins, detectors, on/off switches, dimmer switches, relay switches, feedback loops etc.  that require for their synthesis information-rich, language-based codes stored in DNA. Hierarchical structures have been proved to be best suited for capturing most of the features of metabolic networks (Ravasz et al, 2002). It has been found that metabolites can only be synthesized if carbon, nitrogen, phosphor, and sulfur and the basic building blocks generated from them in central metabolism are available.

This implies that regulatory networks gear metabolic activities to the availability of these basic resources.  So one metabolic circuit depends on the product of other products, coming from other, central metabolic pathways, one depending from the other, like in a cascade.  Further noteworthy is that Feedback loops have been found to be required to regulate metabolic flux and the activities of many or all of the enzymes in a pathway.  In many cases, metabolic pathways are highly branched, in which case it is often necessary to alter fluxes through part of the network while leaving them unaltered or decreasing them in other parts of the network (Curien et al., 2009). These are interconnected in a functional way, resulting in a living cell. The biological metabolic networks are exquisitely integrated, so the significant alterations in inevitably damage or destroys the function. Changes in flux often require changes in the activities of multiple enzymes in a metabolic sequence. Synthesis of one metabolite typically requires the operation of many pathways.

Conclusion:   Regardless of its initial complexity, self-maintaining chemical-based metabolic life could not have emerged in the absence of a genetic replicating mechanism ensuring the maintenance, stability, and diversification of its components. In the absence of any hereditary mechanisms, autotrophic reaction chains would have come and gone without leaving any direct descendants able to resurrect the process. Life as we know it consists of both chemistry and information.   If metabolic life ever did exist on the early Earth, to convert it to life as we know it would have required the emergence of some type of information system under conditions that are favorable for the survival and maintenance of genetic informational molecules. ( Ribas de Pouplana, Ph.D.)



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

The number of electrons (in the universe) is equivalent to the number of protons to an accuracy of one part in 10 to the 37th power. If it were not so, galaxies, stars, and planets would never form (because electromagnetic forces would so overwhelm gravitational forces).
So what does one part in 10 to the 37th power look like? Imagine the entire North American continent covered in dimes, and that continent-wide pile of dimes reaching all the way to the moon. Now, consider a million such continent-wide, to-the-moon-high stacks of dimes, and among all those dimes a single one painted red. One part in 10 to the 37th power is like a blind-folded person successfully selecting that one red dime on the first try!
Morons might not be amazed by this fact - i am !!



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

What is absolutely nothing good for? It's good for absolutely nothing. It' can't do something, nor know something. It can't change something, nor cause something, nor turn its condition of absolutely nothing into something. If there were absolutely nothing past eternity, then that would not change forever. It would always remain and keep being none being. From nonbeing, being cannot emerge. There had to be something beyond the universe, in order for us to be here and philosophize about absolutely nothing. Since that something had to be able to decide to change something, that something had to be a conscious being, unconstrained and free to provoke change. Since it created energy, it had to be powerful. Powerful enough to create our universe, and have power above the power/energy of our universe. Since that being had to be eternal, the energy and power it commands have to be eternal too, and not constraint to physical laws like thermodynamical laws. Gods power is eternal and part of his essence. For this reason, he can promise us eternity, and that we might be eternal with him.




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

Artificial intelligence and humanoids, compared to the human body

DESIGN PRINCIPLES of a human mimetic humanoid
The fundamental concept underlying our design is to consider the human mechanism, which contrasts with the conventional engineering approach used in the design of existing humanoids. For at least the last two millennia, human beings have endeavored to understand the systems and mechanisms that make up the human body, such as the principles of muscle control, the sensory nervous system that connects the brain and the body, the mechanisms of learning in the brain, and the accomplishment of the simple act of walking.
http://robotics.sciencemag.org/content/2/13/eaaq0899

Kenshiro is the most advanced Human humanoid MADE IN JAPAN. mimetic humanoid DESIGN CRITERIA were on the basis of the mechanisms in the human body. Its musculoskeletal systems are as close as possible to that of a human.  The researchers in Japan have been refining robotic parts to mimic human parts and assembling them to make whole robots that move as closely as possible to the ways humans move.
https://techxplore.com/news/2017-12-team-japan-advanced-humanoid-robot.html

“These robots are inherently cross-disciplinary, involving advanced locomotion and manipulation, biomechanics, artificial intelligence, machine vision, perception, learning and cognitive development, as well as behavioral studies.
https://www.telegraph.co.uk/science/2017/12/20/human-like-robots-yet-able-play-badminton-perform-sit-ups-blessed/

2017 PAL Robotics launches TALOS, a fully electrical humanoid robot with joint torque sensors and EtherCAT communication technology that can manipulate up to 6Kg payload in each of its grippers.
https://en.wikipedia.org/wiki/Humanoid_robot

SMARTLY DESIGNED Carefully crafted
http://blog.pal-robotics.com/talos-robot-the-new-humanoid-from-pal-robotics/

Biomimetics
http://reasonandscience.catsboard.com/t1520-biomimetics

The evidence of the imitation
1. The hard work of the scientists to find and make the complex designs of nature is seeing and imitating the creation of the first creator who already created everything in a very good manner, a long time ago.
2. Thus, God the primeval supreme most probably, designer exists.

The smart money is on biomimetics, a hot new trend built on intelligent design principles, assuming, as it does, that nature's designs are so good they are worth imitating. If any investors want to send even a small portion of Lonsdale's promised funding to support biomimetics projects or intelligent design organizations, such as Biologic Institute, Discovery Institute or Illustra Media, they can rest assured it won't take 150 years to show some returns.

It took humanity two thousand years, and the best minds to conceptualize and develop human-like robots, which are despite all the intelligence employed to create them, far from close to the complexity and perfection of the human body.

The human body:
When we arrive on this earth we are endowed with the most perfect, the most efficient, and the best-constructed machine ever devised – our body. A machine beautifully engineered and constructed with the best materials with no planned obsolescence. Constructed with material of superb quality destined with proper use to last long periods of time.

The body's computer, the brain, is by far the most sophisticated, the finest constructed, the most efficient computer that has ever been or ever will be designed. No man-made computer can approach the efficiency of the computer each of us has.

- 37,2 trillion Cells
- each human Cell hosts 2,3 billion molecular machines ( proteins )
- The  human brain: 86 billion neurons
- The bit capacity of the human brain:  10^8,342 bits , exceeds the bit capacity of the entire universe at 10^120 bits
- the storage capacity of one human brain is equivalent to 10^8,419 modern computers
- the human brain’s memory capacity:  1,000 terabytes (for comparison, the 19 million volumes in the US Library of Congress represents about 10 terabytes of data)

http://reasonandscience.catsboard.com/t2697-topics-on-the-structural-complexity-of-the-human-body?highlight=human

No intelligence required to make it?

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

Atheists & wasting time

Every atheist that want to argue and debate me, should be prepared. He should know that I enter NEVER a debate because I am open-minded towards atheism. I am not. I am close-minded. As close-minded as it can get. You can call me a fundamentalist and non-tolerant. and indeed. I am. I do not know why I should even consider atheism to be true when I know it is not. So, if, dear atheist, it is your aim to convince me that your views might be true, and have some value to be considered, let me tell you before you waste your time on me: You won't leave the debate with a smile on your face, believing that you won, or that you might have been able to change my position one jota. You won't. You will leave with the sentiment that you did not reach anything. And that is true. You will NOT be able to convince me that God can be dismissed and that he is not necessary to explain our existence. I think I am doing a great service to you by telling you that, so in case your aim is to convert me to the empty gospel of nothing and drag me down to your ignorance and unbelief, you can save your time to watch " Ren & Stimpy "Adult Party Cartoon". You will feel that you employed your time better. But let me tell you.

I will let a small door open for you.

There are TWO things that would change my mind. You can try. Demonstrate me the bones of Jesus in the grave, like in the movie " The body " with Antonio Banderas, and you have destroyed my faith in the resurrected Jesus, and I commit to wire you us$ 1.000.000,00. Let me write that in extended letters: ( ONE million dollars ). HEY, you can become a millionaire !!

Secondly, you can meet my burden of proof, and falsify my claim that factories and machines cannot self-assemble. The only thing you need to do is an in vitro laboratory experiment in one of the University's dedicated to Abiogenesis research, and turn the basic chemical compounds that are required for life into a self-replicating cell. The simplest one is enough. If you can do that, I promise, I will get in touch with the Nobel prize organization in Stockholm and indicate you for the Nobel prize, and you will become very very famous. Try. Good luck.

And here some reasons, why I believe in God:

125 reasons to believe in God

http://reasonandscience.catsboard.com/t1276-125-reasons-to-believe-in-god

Concluding a Creator as the best explanation of our existence is not an argument based on gaps of knowledge and ignorance, but on a solid epistemological framework and sound scientific, philosophical and theological reasoning, and what we do know, discovered and observed in the natural world.

From absolutely nothing, nothing comes. Creation demands an Intelligent Designer. If there were no creator, there would still be nothing. The universe had a beginning and requires, therefore, a cause. The universe cannot be past eternal. This present moment in time can't represent an actual infinite number of events added one to another proceeding from the past. Time has proceeded forward from the past as one event is added onto another to get us to today. But we know that whenever you pause in the count as we've done today, that you can't have an infinite number of events. Which means that there is not an infinite number of events that goes backward from this point in time. Which means the universe is not eternal. The physical laws require a lawmaker. The physical universe and its laws are interdependent.

There are over 150 finely tuned constants of the universe that must be all just right to the extreme. The expansion rate of the Big bang, the cosmological constant, the four fundamental forces, and the earth, are fine-tuned and require a tuner. It is astonishing to say the least, that the number of electrons (in the universe) is equivalent to the number of protons to an accuracy of one part in 10 to the 37th power. If it were not so, galaxies, stars, and planets would never form. Quarks and anti-quarks form via matter-antimatter pair production. Because of their nature, these particles instantly annihilate each other. However, during the Big Bang, a slight asymmetry in this pair production resulted in approximately 1 extra particle of matter for every 10 billion produced. It turns out that this 1 in 10 billion ratio of “leftover particles” happens to be the exact amount of mass necessary for the formation of stars, galaxies, and planets. As much as 2 in 10 billion, and the universe would have just been filled with black holes. As little as 0.5 in 10 billion, and there wouldn’t have been enough density for galaxies to form.

Life comes only from life. How is the origin of these things best explained? Supercomputers, hardware, software based on a language using signs and codes like the alphabet, an instructional blueprint, complex machines, factory assembly lines, error check and repair systems, recycling methods, waste grinders and management, power generating plants, power turbines, and electric circuits ? Randomly, by unguided, accidental events, or intelligent invention, planning, design, and implementation? Chance is the ONLY causal alternative, once design is excluded, to explain the origin of biological Cells, which are literally miniaturized, ultracomplex, molecular, self-replicating factories. Conscience, free will, morality, human values, logic, speech, the mind, and beauty are also all best explained through design. Based on evidence and observation, it makes the most sense, and it is rational to conclude that the probability is far far higher, that the natural world was created, rather than not. That is not an argument of ignorance but based on positive scientific evidence.

The day when scientists discovered that the universe most probably a beginning, it was doomsday for naturalism. Even more, when unprecedented evidence elucidated the shocking and incredible fact that the universe, from the quantum to the macro scale, was adjusted in the extreme to make life possible on earth.
When it became clear, that DNA stores codified information, as well. When it became clear, that biological Cells are miniaturized factories, the funeral bells for a worldview without God where ringing. And so, when science became slowly to realize that Darwin's idea was a fluke.

Nonetheless, atheists are singing, mocking, rattling their instruments, blowing their trumpets, organizing marches for humanism and secularism, celebrate their stars, open temples to express their unbelief, name calling who defies them and doing nothing else than expressing their brainless blindness. What a strange world in which we live.....

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117 Re: My articles on Sun Aug 12, 2018 4:42 pm

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To be or not to be. That is the question.

Was it chance or was it a mind?
Did God say, “Let the land produce living creatures according to their kinds", or was just chance and coincidence around the block, scrambling, mixing, concentrating, and giving chemical reactions plus a nice portion of time alchemistic powers to turn nonlife to life?
Humankind advanced, and enlightenment emerged, and inquiring minds asked:
"Mirror Mirror on the wall, who's the smarter and more capable of the two?" Is it chance, or is it God?

The mirror answered:
"Chance, you are the fairest here,
But the Lord, old of age, and infinite in power and wisdom, is still a trillion times smarter than you. "

Then Lady coincidence uttered a curse and was so afraid of her, so afraid that she did not know how to let herself go. At first, she did not want to keep promoting herself, but she did not rest, she had to go and keep influencing the human mind for another 150 years. And as she entered the 21th century, she recognized the warriors of Christ, and in terror she stood there, unable to move. But lie tests were already placed over coal fire and carried in with tongs and placed in front of her. Then she had to step forward and do the lie test, and dance until she fell dead to the ground. Her lies were exposed and unmasked. Humankind could not keep being deluded by her. Lady Chance & coincidence was forever gone.

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118 Re: My articles on Fri Sep 07, 2018 2:59 pm

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The Carbon Cycle, how it points to intelligent design

In photosynthesis, oxygen is produced and released into the atmosphere, and carbon dioxide in an opposite process is fixed.

Lehninger, Principles of Biochemistry, 5th ed.
The oxygen-evolving complex produces oxygen by splitting water in an enormously complex process where quantum mechanics is employed. Science even today does not fully understand the process. Subsequently, the process drives the make of ATP by ATP synthase, and coenzymes are reduced ( energetically charged ) through ATP, which drive the dark reactions of photosynthesis.  Rubisco proteins in the Calvin Cycle fix carbon dioxide from the atmosphere, and the end product is glucose. Glucose is the carbohydrate ( sugar ),  fuel to make ATP in eukaryotic cells, and in the process releases Carbon dioxide into the atmosphere. So the Carbon cycle closes.  

In aerobic respiration, oxygen accepts electrons at the end of the mitochondrial electron transfer chains.  and bound to water, and carbon dioxide is released into the atmosphere: the opposite of what happens in photosynthesis.

Aerobic respiration is a process that occurs in three stages, namely the first stage is glycolysis, the second stage occurs in the Krebs cycle inside of mitochondria, where carbon dioxide is released, and in the third stage, electron transfer phosphorylation, the coenzymes reduced ( energetically charged ) during glycolysis and the Krebs cycle ( the first two stages) deliver electrons and hydrogen ions to electron transfer chains. The H+ gradient that forms across the inner mitochondrial membrane drives the flow of hydrogen ions through ATP synthases, which results in ATP formation.The energy released by electrons as they move through the chains drives the formation of as many as 32 ATP. At the end of the electron transfer chains, water forms when oxygen accepts hydrogen ions and electrons. ATPs fuel all the processes in the Cell, amongst it, the make of proteins.

This is an interdependent process, and naturalistic explanations how everything gradually emerged is a true festival of pseudoscientific mambo-Jambo, full of guesswork, and just so stories.

Another remarkable fact is that  ATP participates in almost all cellular reactions, so a cell benefits from making a lot of it. However, aerobic respiration is a dangerous occupation. When an oxygen molecule (O2) accepts electrons from an electron transfer chain, it dissociates into oxygen atoms. Most of the atoms immediately combine with hydrogen ions and end up in water molecules. Occasionally, however, an oxygen atom escapes this final reaction. The atom has an unpaired electron, so it is a free radical.

Mitochondria cannot detoxify free radicals, so they rely on antioxidant enzymes and vitamins in the cell’s cytoplasm to do it for them. The system works well, at least most of the time. However, a genetic disorder or an encounter with a toxin or pathogen can tip the normal cellular balance of aerobic respiration and free radical formation. Free radicals accumulate and destroy first the function of mitochondria, then the cell. The resulting tissue damage is called oxidative stress.

At least 83 proteins are directly involved in mitochondrial electron transfer chains. A defect in any one of them—or in any of the thousands of other proteins used by mitochondria—can wreak havoc in the body. New research is showing that oxidative stress caused by mitochondrial malfunction is also involved in many other illnesses, including cancer, hypertension, Alzheimer’s and Parkinson’s diseases, and even aging.

Lehninger, Principles of biochemistry, fifth ed. page 22
Autotrophs and heterotrophs participate in global cycles of O2 and CO2, driven ultimately by sunlight, making these two large groups of organisms interdependent.

Question of course arises: What emerged first: antioxidant enzymes, or aerobic respiration? Once again, you can imagine how secular science papers struggle to explain it....

You can have an idea and taste, here:

Evolution of oxygen utilization in multicellular organisms and implications for cell signalling in tissue engineering
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3258841/

The defence mechanisms against these toxic elements ARE THOUGHT  to have evolved before the rise in oxygen levels that allowed for aerobic respiration. If these mechanisms had not been in place, there could have been deleterious effects on the first oxygen-respiring organisms. For example, cytochrome oxidase, the catalyst in oxygen to water reduction, was found before oxidative phosphorylation began. In addition, carotenoids, which do not require oxygen for their production and are produced by anaerobes, protect against the effects of H2O2. What led to the appearance of these elements prior to the rise in oxygen is unknown, but a source other than oxygen itself must have driven the process. Once oxygen levels rose, further defence mechanisms evolved.

Can such guesswork be called science ??

A nice pdf on the subject:
http://www.mhhe.com/biosci/genbio/raven6b/graphics/raven06b/other/raven06b_10.pdf



Global cycles of oxygen and carbon energy cycles, and nitrogen cycles, point to interdependence and irreducibility of autotrophic and heterotrophic forms of life

Photosynthesis and cellular respiration are important cell energy processes. They are connected in ways that are vital for the survival of almost all forms of life on earth.

Nearly all living organisms derive their energy, directly or indirectly, from the radiant energy of sunlight. The light-driven splitting of water during photosynthesis releases its electrons for the fixation of oxygen dioxide (CO2) and the release of oxygen (O2) into the atmosphere. Carbon fixation or сarbon assimilation is the conversion process of inorganic carbon (carbon dioxide) in the air to organic compounds by living organisms.

While some autotrophic organisms are photosynthetic and obtain their energy from sunlight,  heterotrophic organisms obtain their energy from the degradation of organic nutrients produced by autotrophs. In our biosphere, autotrophs and heterotrophs live together in a vast, interdependent cycle in which autotrophic organisms use atmospheric carbon dioxide to build their organic biomolecules, some of them generating oxygen from water in the process. Heterotrophs, in turn, use the organic products of autotrophs as nutrients and return carbon dioxide to the atmosphere.

Some of the oxidation reactions that produce carbon dioxide also consume oxygen, converting it to water. Thus carbon, oxygen, and water are constantly cycled between the heterotrophic and autotrophic worlds, with solar energy as the driving force for this global process.

In addition to the global carbon and oxygen cycle, a nitrogen cycle operates in the biosphere, turning over huge amounts of nitrogen. In the biosphere, the metabolic processes of different species function interdependently to salvage and reuse biologically available nitrogen in a vast nitrogen cycle.

The cycling of carbon, oxygen, and nitrogen, which ultimately involves all species, depends on a proper balance between the activities of the producers (autotrophs) and consumers (heterotrophs) in our biosphere.

How did this proper balance first emerge? To me, it is clear evidence, that it had all to emerge together, all at once, at one specific moment back in the past, and as such, evidence of sudden creation. and not evolutionary deep time. 

Energy cycles, how did they "take off" ?
http://reasonandscience.catsboard.com/t2660-energy-cycles-how-did-they-take-off



Last edited by Admin on Sat Sep 08, 2018 7:33 am; edited 7 times in total

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When mainstream textbooks hijack evolution....

Lehninger, Principles of Biochemistry, 5th ed. page 26
Metabolism would be better represented as a web of INTERCONNECTED and INTERDEPENDENT pathways. A change in the concentration of any one metabolite would start a ripple effect, influencing the flow of materials through other pathways. The task of understanding these complex interactions among intermediates and pathways in quantitative terms is
daunting, but the new emphasis on systems biology,, has begun to offer important insights into the overall regulation of metabolism.

page 419:
Animal cells exchange information about the concentrations of ions and glucose in extracellular fluids, the INTERDEPENDENT metabolic activities taking place in different tissues, and, in an embryo, the correct placement of cells during development.

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The marvel of self-folding machines, and origin of life scenarios

Researchers at MIT’s Tangible Media Group have developed a self-folding, origami-like technology called aeroMorph. The project showcases a design, simulation, and fabrication pipeline for making transforming objects. Autonomous self-assembly of functional machines from flat sheets is possible with a composite that folds itself.

https://www.youtube.com/watch?v=LsCmG6O0Eo4


The new type of inflatable could open the door to all sorts of things—basically, whatever designers figure out they can create with the material. Origami can turn a sheet of paper into complex three-dimensional shapes, and similar folding techniques can produce structures and mechanisms. Self-assembly of folding two-dimensional materials into three-dimensional (3D) structures is particularly useful since it permits to employ 3D structures into a far wider range of applications. To demonstrate the application of these techniques to the fabrication of machines, they developed a crawling robot that folds itself. The robot starts as a flat sheet with embedded electronics and transforms autonomously into a functional machine. To accomplish this, they developed shape-memory composites that fold themselves along embedded hinges.

They used composites to recreate fundamental folded patterns, derived from computational origami, that can be extrapolated to a wide range of geometries and mechanisms. This origami-inspired robot can fold itself in 4 minutes and walk away without human intervention, demonstrating the potential both for complex self-folding machines and autonomous, self-controlled assembly.

My comment:
I don't doubt you will recognize such a robot as an engineering marvel. It could evidently not be created without investing considerable time to know about the appropriate materials, how they behave, and what it would take to fold in a predictable manner. Then, it has to be learned what kind of folding the material can perform, and what forms it can endorse.  

Specifically, the researchers discovered that this composite material can be used to build a self-folding crawling robot that represents both a complex structure and a functional device that demonstrates three capabilities of the composite:

(i) producing complex shapes,
(ii) producing dynamic mechanisms, and
(iii) assembling autonomously

The composite includes self-folding hinges that are controlled by embedded heating elements. So knowledge is required to know at what temperatures the folds occur. The placement of these hinges in the composite and the order in which they are triggered create a fold pattern that determines the final shape of the 3D structure or mechanism.  PSPS is a shape-memory polymer that is mechanically programmed to contract bidirectionally when heated to approximately 100°C.

My comment:
Let us suppose, the researchers want to develop 3D structures with these materials that fold into even more complex structures, but machines that help to fold correctly are required. So then, they would have to sit down again, and investigate, and develop these machines which are performing the right actions to help in the folding process. It is evident, that this would constitute an even higher level of complexity and order.


What I just described, is not new. But employed in the molecular world, and essential for life to exist. Above is nothing more or less, than one more example of biomimicry. 

Proteins are polymers or chains of 20 different amino acids. Each of these amino acids does have specific properties, based on their various side chains, the so-called R group, that gives each amino acid its identity. Amino acids can be positive, negative, polar, or non-polar, which permit them to have various chemical functionalities, and either repeal or attract water. Specific protein shape, and the folding of linear polymer chains into complex 3D forms and conformation depends on the interactions between the amino acid sequence, composition, their side chains interactions, but also on the temperature of the surrounding, amongst other things.  For a protein to function it must fold into a resting state which is a complex three-dimensional structure. To find functional sequences that adopt useful 3D forms would if chosen randomly, be impossible. Chance would have to select to find a functional sequence of a chain with 100 amino acids, amongst 10^73 possible sequences. That is almost the number of atoms in the entire universe. 

Molecular information is the information found in a gene. Information has a precise mathematical definition as defined by information theory. Molecular Knowledge is the minimum amount of useful information required by a gene  to instruct the ribosome factory to create correct amino acid polymers which fold into functional proteins with functional 3D forms.

A minimal amount of information is required to make a functional protein. A minimal number of amino acid monomers chained together are required to make a functional protein. So, safely it can be said:  EVERY PROTEIN IS IRREDUCIBLY COMPLEX. Only once it reaches the threshold of functionality, further mechanisms can change it upon external ecological pressures, to adapt, or evolve upon various evolutionary mechanisms. Be they preprogrammed, or upon a very limited range of mutations and natural selection.

EVOLUTION IS NOT A POSSIBLE MECHANISM TO EXPLAIN THE ORIGIN OF THE MINIMAL INFORMATION TO CREATE THE FIRST, SIMPLEST LIFE-FORMS. 

In cells, many proteins require the assistance of molecular chaperones for their folding.  Molecular chaperones are key players in the maintenance of proper protein folding and overall proteostasis. Chaperones are required by newly synthesized proteins to ensure both accurate folding and to prevent aggregation. Indeed, chaperones function both cotranslationally and in times of cellular stress, Chaperones are found in all types of cells and in every cellular compartment. They bind to target proteins to facilitate proper folding, prevent or reverse improper associations, and protect their accidental degradation. They are also involved in many macromolecular assembly processes, including the assembly of nucleosomes, protein transport in bacteria, assembly of bacterial pili, binding of transcription factors, and ribosome assembly in eukaryotes. A subset of molecular chaperones has even been implicated in signal transduction. This follows upon the discovery that steroid hormone receptors, which are cytoplasmic proteins, combine not only with their respective hormones but also require chaperones in order to form functioning recycling complexes.

When a polypeptide, or chain of amino acids, emerges from the ribosome translation factory on its way to becoming a protein, it looks like a useless, shapeless piece of string.  It cannot perform its function till folded into a precise, compact shape particular for its job.  Some short polypeptides will spontaneously fold into their “native” state, ready for work, but many of the bigger ones need help.  Fortunately, the cell provides a private dressing room called the GroEL-GroES chaperonin that not only gives them privacy, away from the bustle of colliding molecules in the cytoplasm but actually helps them get correctly folded.  This chaperone or “helper” machine thus not only gets the actor ready for the stage faster but prevents misfolding that could clutter the cell with useless or harmful aggregates of protein. 

The inside walls of the GroEL barrel and the inside walls of the GroES lid contain protrusions that generate electrostatic and hydrophobic forces on the interior space.  When the unfolded protein enters, therefore, it is subjected to gentle pressures that coax it to fold.  These forces are nonspecific enough to work on hundreds of different substrates that use this general-purpose machine.   The forces change during the entry of the nascent protein.  The interior is not barrel shaped when the actor approaches the door; the GroES lid, with the help of the energy molecule ATP, guides the protein in, and then the barrel pops into its shape, providing a safe haven for folding.  The electronic walls turn on to provide that gentle nudge to get the polypeptide over its energy barriers and into the right folding pathway.  When the protein has properly completed its folding after about 10 seconds, the door opens and the protein pops out, ready for operation.

Chaperonins are an engineering marvel. Each GroEL Chaperone protein subunit has a binding pocket for ATP , which releases its energy, and subsequently, undergoes a conformational change that widens and elongates the inner cavity so as to more than double its volume. The expanded cavity can enclose a partially folded substrate protein. All seven subunits of the GroEL ring act in concert; that is, they are mechanically linked such that they change their conformations simultaneously. The  rings undergo conformational changes in a reciprocating fashion, with events in one ring influencing events in the other ring. 

How finely tuned is this machine?  The authors did some experiments on mutating the chaperone to make the barrel looser and tighter.  They found that volume changes as small as 2-5% slowed down the folding considerably. The barrel volume needs to be within certain narrow limits, yet general enough to handle a variety of small, medium and large proteins. 

The GroEL/GroES nano-cage allows a single protein molecule to fold in isolation.  This reaction has been compared to spontaneous folding at infinite dilution.  However, recent experimental and theoretical studies indicate that the physical environment of the chaperonin cage can alter the folding energy landscape, resulting in accelerated folding for some proteins.  By performing an extensive mutational analysis of GroEL, we have identified three structural features of the chaperonin cage as major contributors to this capacity: 

1. geometric confinement exerted on the folding protein inside the limited volume of the cage; 
2. a mildly hydrophobic, interactive surface at the bottom of the cage; 
3. Clusters of negatively charged amino acid residues exposed on the cavity wall. These features in combination provide a physical environment that has been optimized to catalyze the structural annealing of proteins with kinetically complex folding pathways.  Thus, the chaperonin system and its mutant versions may prove as useful tools in understanding how proteins navigate their energy landscape of folding.

What we see here are molecular machines working with precision, efficiency, control – and design. Protein folding is a complex affair, wherein several domains of the polypeptide fold sequentially or simultaneously following an energy landscape (like a pinball negotiating obstacles) that leads to the completed protein. Some domains fold into a helix or sheet, or several, which then combine into larger structures.  Even then, after the protein exits the chaperone, there can be subsequent modifications: multiple proteins, for instance, might be joined into complexes, with metal ions inserted (as in hemoglobin or chlorophyll), and these proteins usually become part of networks.  Add to that now the exciting discovery that the walls of the chaperone barrel are interactive, coaxing the proteins to fold properly. At every stage, there is coordinated, synchronized, elegant design. Think about how these molecules operate in the blind.  They do not have eyes and brains telling them where to go – yet they succeed.  There is no analog in human technology; the closest, perhaps, is computer programming, but in life, at scales smaller than most of us can imagine, nano-factories operate with physical entities moving through space and time.  How fortunate we are to see these marvels unfold.  Our ancestors might have wondered at the mysteries of biological life, but could they in their wildest dreams have imagined the city-like organization at work at the molecular level?

The versatility of these helper-proteins is substantially due to precise localization within the cell and the specificity of substrate protein binding. These interactions fine-tune, in critical ways, the ability of chaperones to participate in diverse cellular processes.

Question: How did these proteins get finely tuned to exercise their functions? Trial and error? Evolution? How could it be by evolution, if intermediate stages would confer no function?
 
Secular science papers admit the fundamental importance of Chaperones in all domains and life, and suggest that a so-called Ur-Chaperonin was likely present in LUCA.  Chaperones are necessary as well for the minimal proteome set for life to kick-start, which makes the hypothesis of an unguided, random naturalistic origin even more unrealistic. 

Another paper reports: The general function of chaperones in assisting protein folding is significant in facilitating the structural evolution of proteins. 

My comment: Science papers often explain biological function in language that sounds suspiciously teleological. This is a nice example. Did early earth have the foresight to see that Chaperone proteins would be necessary to assist protein folding? and even more, that energy would be required, providing it at the right place, in the right dosage? 


Chaperones are another formidable example of intelligent design in the molecular world, which contributes making it entirely irrational to infer random natural mechanisms to explain their existence. God is a logical inference based on the evidence observed in the natural world. Based on current knowledge, an intelligent creative agency is a better explanation than materialistic naturalism. 

A deeper look at Chaperones:
http://reasonandscience.catsboard.com/t2590p25-origins-what-cause-explains-best-our-existence-and-why#6138

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121 Re: My articles on Sun Sep 16, 2018 4:31 pm

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Life is pervaded by goal-orientedness, uniqueness, organization, beauty, stability, fine-tuned regulation, coordination, homeostasis, interdependence from the molecular to macro-eco-systems, kinetic functionality, molecular recognition through structural complementarity, sophisticated information-based manufacturing, and self-replication, permanence, and change, sensitivity, and stimulation, growth, and development. Almost every of the mentioned points is essential and indispensable for life to exist and perpetuate.
Life represents the most dramatic and fundamental of all discontinuities in the natural world, from the chaos and purposelessness of specific geological forms and chemical elements to the teleological; goal oriented, energy requiring, complex specified structures of the living.

It is beyond me, why we should not infer that the living is evidence of the action of an incomprehensible power with limitless foresight, knowledge, and intelligence, rather than chaos, random natural forces without goals, nor external direction.

The more I think about existence, the more it amazes and is incomprehensible to me, why I am, why we are, and much more, why there is such an amazing creator that said: I AM, became flesh, walked amongst us, died for our sins, arose from the dead, demonstrated his love in such a counterintuitive manner, and promised to go and to prepare a place of unimaginable beauty to stay for you. For me. For all of us. Eternally. With him. I want this amazing creator. I want to stay with HIM. Worship HIM. Bow in front of HIM. To know more about HIM. And learn about his amazing creation and discover its hidden treasures.

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

Poo & oxygen !!

When whales do their basic physiological things, in other words, when they poo,  the product serves as nutrients for phytoplankton. And these little organisms are the basis of the oceanic food chain. So when Whales go to the toilet, they release iron in their poo. Iron is taken up by phytoplankton by ultracomplex molecular mechanisms. It is chelated by non-ribosomal peptide synthetases, literal molecular assembly lines on the surface of the host's cell membrane, which bind iron and make the product fit to be transported into the internal phytoplankton cell milieu by highly sophisticated import channel proteins. Ones in the inside, the iron is transported to the assembly site of enzymes. The same occurs with sulfur which is similarly imported. Together with iron, complex molecular machinery builds iron-sulfur clusters, which form the active site of numerous proteins, used in the phytoplankton photosynthesis pathway. Through photosynthesis, carbon dioxide is fixed, and these little organisms make carbon available for all marine life, and so for the existence of fish, and all ocean creatures. At the same time, phytoplankton release oxygen into the atmosphere. To be precise about 50%, which you and I breathe.

You didn't imagine how important Spermwhale poo was for you, did you ??

Essential elements and building blocks for the origin of life
http://reasonandscience.catsboard.com/t2437-essential-elements-and-building-blocks-for-the-origin-of-life

Molybdenum, essential for life
http://reasonandscience.catsboard.com/t2430-molybdenum-essential-for-life

Biosynthesis of Iron-sulfur clusters, basic building blocks for life  
http://reasonandscience.catsboard.com/t2285-iron-sulfur-clusters-basic-building-blocks-for-life

Sulfur essential for life
http://reasonandscience.catsboard.com/t2433-sulfur-essential-for-life

Iron Uptake and Homeostasis in Cells
http://reasonandscience.catsboard.com/t2443-iron-uptake-and-homeostasis-in-prokaryotic-microorganisms

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

Thermodynamics, and the origin of life

Intelligent design literature has sufficiently explained, that a mind is necessary to produce a language and based on it, complex, specified or instructional information or blueprints, which can be used to make specific purposeful artifacts, or in case of life, a creator had to store the information contained in DNA to make life ( See the excellent books of Werner Gitt, In the beginning, was information, and Signature in the Cell, Stephen C. Meyer )

There is, however, another aspect: In order to produce a system producing information, there must be an energy input to move from a disordered to an ordered state.

Let me explain:

If someone just imagines the sentence

" Please make a cube, the size of 4" x 4" x 5", using teak wood, 0,5" thick "

in his mind and wants to communicate it to someone else in order to make that cube, the instructional sentence has to be written down, for example on a piece of paper which the counterpart can read and understand. Let's suppose there are just random letters on the floor. The sentence quoted above uses about 50 letters, so these, the right ones, had to be lying around, ready to be picked up. Maybe not all extant alphabetic letters are used, so only the needed ones have to be selected. The right letters, one by one, would have to be chosen, be picked from the floor, and lined up in the right order and sequence. Once done, someone else could read and understand the sentence. But for this to happen, someone has to a) select the letters on the floor, b) pick them up, and c) put them in the right place and the right order. Energy and work is required to perform this action. In the case of humans, the contraction of muscles requires oxygenic respiration in mitochondria and the consumption of energy in the form of ATP on a molecular level of muscle cells.

So establishing the flow of information depends not only on hardware and software, ( an information storage device, and the stored instructional blueprint ), but also on the transfer of energy to perform the exchange from a disordered state ( random letters on the floor ) to a ordered state - an informational sentence ( the ordered sequence of letters, correctly lined up that form the phrase ).

The same occurs in living organisms. Energy input in the form of ATP is required to produce information-rich, organized structures such as proteins and nucleic acids. An essential Origin of Life research problem is not only the availability of the basic building blocks of life on a prebiotic earth but how could they have been brought and concentrated to one construction site, where they would all have been available at the same time, and then put into the right order to create information, according to the secular narrative, first through the formation of RNA polymers, which in sequence, began self replication.

http://reasonandscience.catsboard.com/t2590-origins-what-cause-explains-best-our-existence-and-why#5811
The emergence of concentrated suites of just the right mix thus remains a central puzzle in origin-of-life research.

That is not a trivial task, but science has no compelling hypothesis how that could have occurred. Fred Hoyles Tornado sweeping through a Junkyard, unjustly dismissed by naturalists, is a good analogy. In the engineering lab of Boeing, the formation of a blueprint to make 747's would hardly emerge by random forces of ink and paper or self-forming computer-aided design, but by the precise order of writing down information by the guiding hand of highly skilled, trained and intelligent engineers, that would store the instructional information that is transmitted to the factory to the workers to make the airplanes.

On early earth, the basic chemical elements would have, somehow, to be transformed, non enzymatically, without the aid of molecular machines that would speed up the process, into the essential molecules of life, namely amino acids, sugars, fatty acids, and nucleotides. Biological Cells use highly complex assembly lines to make these essential basic molecules. ( In our analogy, the letters for the informational sentences have to be formed from raw materials ) Life uses ultracomplex metabolic pathways, and a myriad of enzymes, but these pathways were non-existent on early earth. To perform just ONE of seven reactions to make pyrimidines, one of the two types of bases to make RNA and DNA nucleotides, enzyme expert Dr Richard Wolfenden, of the University of North Carolina, showed in 1998 that the reaction performed by OMP decarboxylase enzymes, is ‘“absolutely essential” in creating the building blocks of DNA and RNA, would take 78 million years in water’, but was speeded up 10^18 times by that enzyme. ( it is the fastest enzyme known ) If by some unknown event, prebiotic mechanisms would have produced the intermediate product, Orotidine 5'-monophosphate, until nonenzymatic reactions would have transformed it into uridine monophosphate, the last product in the pathway, after 78mio years, the molecule would have disintegrated long ago by ultraviolet light and other environmental factors.

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

Science cannot explain how the basic essential molecules emerged prebiotically, and the proposals are fantasies at best and range from panspermia to hydrothermal vents, and so on. None of the attempted explanations are compelling, or conclusive.

But let us suppose, even that these essential molecules would be all there, in the right concentration, at one site, ready to be assembled into informational biomolecules. If there were no energy to arrange them together, no deal. The energy would have to be channeled to the right place, but a sweeping tornado would cause only chaos.

Eugene Koonin brings it straight to the point:
" A succession of exceedingly unlikely steps is essential for the origin of life, from the synthesis and accumulation of nucleotides to the origin of translation; through the multiplication of probabilities, these make the final outcome seem almost like a miracle. The difficulties remain formidable. For all the effort, we do not currently have coherent and plausible models for the path from simple organic molecules to the first life forms. Most damningly, the powerful mechanisms of biological evolution were not available for all the stages preceding the emergence of replicator systems. Given all these major difficulties, it appears prudent to seriously consider radical alternatives for the origin of life. Notwithstanding relevant theoretical models and suggestive experimental results, we currently do not have a credible solution to these problems and do not even see with any clarity a path to such a solution. "

and Bill Faint
" Life in any form is a very serious enigma and conundrum. It does something, whatever the biochemical pathway, machinery, enzymes etc. are involved, that should not and honestly could not ever "get off the ground". It SPONTANEOUSLY recruits Gibbs free energy from its environment so as to reduce its own entropy. That is tantamount to a rock continuously recruiting the wand to roll it up the hill, or a rusty nail "figuring out" how to spontaneously rust and add layers of galvanizing zinc on itself to fight corrosion. Unintelligent simple chemicals can't self-organize into instructions for building solar farms (photosystems 1 and 2), hydroelectric dams (ATP synthase), propulsion (motor proteins) , self repair (p53 tumor suppressor proteins) or self-destruct (caspases) in the event that these instructions become too damaged by the way the universe USUALLY operates. Abiogenesis is not an issue that scientists simply need more time to figure out but a fundamental problem with materialism ".

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122 Pseudo-science in science papers on Mon Sep 24, 2018 8:07 am

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Pseudo-science in science papers

The scientific establishment and education system induce students and people in general to trust science, and the respective science papers and books. And so, subsequently, to trust the philosophical framework upon which it is grounded, which is, philosophical and methodological naturalism. The scientific literature is permeated by pseudo-scientific claims, in order to press the evidence seen in nature in they're a priori assumptions of naturalism.

The make of pseudoscience

http://reasonandscience.catsboard.com/t1993-the-make-of-pseudo-science

When certain biologists discuss the early stages of life there is a tendency to think too vaguely. They see a biological wonder before them and they tell a story about how it might have come to be. They may even draw a picture to explain what they mean. Indeed, the story seems plausible enough, until you zoom in to look at the details. I don't mean to demean the intelligence of these biologists. It's just that it appears they haven't considered things as completely as they should. Like a cartoon drawing, the basic idea is portrayed, but there is nothing but blank space where the profound detail of biological processes should be.

Following, a  nice example:

In the paper: Information as a Manifestation of Development :

http://sci-hub.tw/http://www.mdpi.com/2078-2489/2/1/102

the authors claim:  

" It is probable that early in the evolution of life,  storing and reproducing information was carried out by RNA and later co-opted by DNA ".

I respond to such pseudo-scientific nonsense a categorical and angry NO !!!!

There is so much WRONG with that sentence. Early in the evolution of life induces to believe that the origin of life was due to evolution.

Then : DNA co-opted RNA's job !!!  Seriously ???? and - why is that PROBABLE ???!!!

First of all: there is NO scientific HYPOTHESIS of the supposed transition from RNA world to DNA world. NONE. nada. NJET. Science DOES NOT KNOW how that supposed transition could have occurred. So to claim that it is probable is a deceptive claim that induces the uninformed reader to put confidence in the authors claim. The informed reader will immediately recognize the claim as a fraud.

The synthesis of Thymine DNA starting with RNA is EXTREMELY COMPLEX, and one of the inumerous reasons why abiogenesis is a FAILED HYPOTHESIS.  I will outline below what that transition requires, so you can have an idea by yourself:

http://reasonandscience.catsboard.com/t2028-the-dna-double-helix-evidence-of-design#6091

Uridine monophosphate (UMP) is a monomer in RNA, and the starting point of the transition from RNA to deoxythymidine monophosphate (dTMP) , or Thymidine, one of the four nucleotides used in DNA.

Once Uridine Monophosphate is synthesized, the further steps are

ribonucleotide reductase
nucleoside diphosphate kinase
dUTP phosphatase ( dUTPase)
thymidylate synthase
thymidylate triphosphate (dTTP)

thymidylate synthase requires:

serine hydroxymethyltransferase (SHMT)
thymidylate synthase (TS)
dihydrofolate reductase (DHFR)

and as co-factor:

N5, N10-methylenetetrahydrofolate

Tetrahydrofolate (H4 folate)has fundamental importance for the biosynthesis of purines, pyrimidines, and several amino acids.

How Do Organisms Synthesize Amino Acids?
http://reasonandscience.catsboard.com/t2590p25-origins-what-cause-explains-best-our-existence-and-why#5938

The synthesis of this cofactor, N5, N10-methylenetetrahydrofolate, requires:

vitamin folic acid (folate)

The two essential precursors of folate biosynthesis are 4-aminobenzoate (a product of shikimate biosynthesis pathway) and GTP

The Shikimate pathway depends on following enzymes:

http://reasonandscience.catsboard.com/t1740-origin-of-the-canonical-twenty-amino-acids-required-for-life#5939

DAHP synthase
3-dehydroquinate synthase
5-Dehydroquinate Synthetase
Shikimate dehydrogenase
Shikimate kinase
3-enolpyruvylshikimate-5-phosphate synthase
Chorismate synthase

and GTP is Guanosine-5'-triphosphate (GTP), a purine nucleoside triphosphate. It is one of the building blocks needed for the synthesis of RNA during the transcription process.

The proteins used in the folate biosynthesis pathway are:
http://reasonandscience.catsboard.com/t2590p25-origins-what-cause-explains-best-our-existence-and-why#5942

GTP cyclohydrolase I (GTPCH)
Dihydroneopterin aldolase (DHNA)
6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase  (HPPK)
Dihydropteroate synthase (DHPS)
folylpolyglutamate synthetase (FPGS)
Dihydrofolate reductase (DHFR)

The conversion of serine to glycine is a prominent means of generating one-carbon derivatives of THF

Biosynthesis of Serine requires following enzymes:

Phosphoglycerate dehydrogenase
Phosphoserine transaminase
phosphoserine phosphatase

Not considering the enzymes to make Nitrogenase for nitrogen fixation and assimilation, almost 30 enzymes are required to make thymidylate triphosphate (dTTP) , one of the nucleotides used in DNA.

And all these enzymes had to emerge prior life could begin. We have described the pathway to make just ONE of the four nucleobases. If someone wants to propose natural unguided processes to make all these molecular machines, the regulation, right interconnection, encoding the information to make each of these hypercomplex enzymes, the odds would be astronomically big. This is a good illustration to demonstrate, why abiogenesis is impossible.

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123 Re: My articles on Wed Oct 03, 2018 6:44 am

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A bouqée of  ten sweet-smelling colorful flowers to unbelievers in a Creator-God

1. The universe is either eternal, or it had a beginning. Most probably it had a beginning, based on philosophical and scientific considerations. Everything which has a beginning has a cause.
2. The Universe had a beginning.
3. Therefore, the Universe had a cause.

1. The physical universe is governed by physical laws, and both, are interdependent and irreducible. There would not be one without the other.
2. Laws and interdependence require a lawgiver.
3. Therefore, the laws of nature require a lawgiver.

1. The initial conditions of the universe, subatomic particles, the Big Bang, the fundamental forces of the universe, the Solar System, the earth and the moon, are finely tuned to permit life. Over 150 fine-tuning parameters are known.
2. The Finetuning is either due to chance, necessity or design.
3. Finetuning is extremely unlikely due to chance or necessity. Therefore, it is most probably due to a powerful creator which did set up the universe in the most precise exact fashion to permit life on earth.

1. Regulation, governing, controlling, recruiting, interpretation, recognition, orchestrating, elaborating strategies, guiding, instruct are all tasks of the gene regulatory network.
2. Such activity can only be exercised if no intelligence is present if the correct actions were pre-programmed by intelligence.
3. Therefore, most probably, the gene regulatory network was programmed by an intelligent agency.

1. DNA stores information based on a code system, and codified, complex, instructional information, with the same function as a blueprint.  
2. All codes and blueprints come from intelligence.
3. Therefore, the genetic code and the instructions to build cells and complex biological organisms, stored in DNA, were most likely created by an intelligent agency.

1. Cells use sophisticated information selection ( the Gene regulatory network ) encoding and transcription ( DNA & RNA polymerase machines ) transmission (mRNA), and decoding ( Ribosome ) systems.
2. Setup of information transmission systems, aka.  Selection, encoding, transmission, and decoding are always a deliberate act of intelligence
3. The existence of the genetic information transmission system is best explained by the implementation of an intelligent designer.    

1. Complex machines and factories are intelligently designed
2. Biological cells are factories full of complex machines
3. Biological cells are intelligently designed...

1. Cells components are part of a complex system that is useful only in the completion of that much larger system. A minimal Cell, in order to make life possible, requires at least 500 interdependent protein - molecular machine complexes fully functional. Basic building blocks and Intermediate biosynthesis products do have no biochemical function on their own, that's why evolution could and would not select them.
2. A discrete minimal size of each individual molecular machine, aka. proteins and holo-protein complexes made of multiple subunits and cofactors are necessary for these to be functional.
3. Each protein and holo-protein requires a minimal size and complexity to be functional. And it has only function interdependently, and correct precise energy supply, and when interconnected with other molecules in the Cell. Irreducibility and interdependence cannot evolve but depend on intelligence with foreknowledge on how to build discrete parts with a distant goal.  

1. Objective logic cannot be based on our subjective minds,a non-static universe or immaterial abstractions outside of a mind.
2. Objective logic exists.
3. Therefore, objective logic is not based on our subjective minds, a non-static universe or immaterial abstractions outside of a mind.

1. If objective moral values exist, then God exists.
2. Objective moral values exist.
3. Therefore, God exists.

Matter-antimatter pair production ratio 1 in 10 billion of “leftover particles” happens to be the exact amount of mass necessary for the formation of stars, galaxies, and planets. The number of electrons (in the universe) is equivalent to the number of protons to an accuracy of one part in 10 to the 37th power. If it were not so, galaxies, stars, and planets would never form. Upon the finetuning by a happy accident of the cosmological constant,  the probability that our universe contains galaxies is akin to exactly 10^123. That is 1 possibility in 1,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000, 000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000 . During one orbit around the Sun, Earth actually rotates about its own axis 366.3 times. The Moon orbits the Earth in 27.3 days. Of course, a day is one Earth rotation on its own axis. 366.3 x 27.3 = 9999.99 At the same time, the Earth is 366.3% the diameter of the Moon and the Moon is 27.3% the diameter of Earth. 366.3% x 27.3% = .999999. The combined diameter of all the planets in our solar system is 10 times greater than the Earth’s circumference. This has astonishingly high accuracy at 99.99%. The distance between the moon and the sun is 400 times greater than the distance from the earth and the moon. The Sun happens to be 400 times the Moon’s diameter, and 400 times as far away. This means the Sun and Moon appear to be the same size when viewed from Earth. The circumference of the earth at the equator is 24,901.55 miles. The earth’s rotation speed is 1037.5646 mph. If you divide 24,901.55 by 1037.5646 you get 24. Which is the number of hours in a complete day. Just enough rotation speed compared to it’s size to equal a perfect exposure to both sun light and darkness so that life could exist here.

125 reasons to believe in God
http://reasonandscience.catsboard.com/t1276-125-reasons-to-believe-in-god

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124 Re: My articles on Thu Oct 04, 2018 6:56 am

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The Histone code, control of Gene Expression, and gene regulatory networks  point to intelligent design

http://reasonandscience.catsboard.com/t2194-control-of-gene-expression-and-gene-regulatory-networks-point-to-intelligent-design

A director of an orchestra has a partiture at hand from the composer, with the instructions codified in notes, on how to direct the orchestra to play a specific composition.

The director of a movie has a script from the author of the story of the movie, which instructs him about the story of the movie etc.

In biology, the expression of genes at the right time, at the right place, is directed by the gene regulatory network.

Essential players are transcription factor proteins, which bind at the right place on the gene, and signal to the transcription machinery which produces an RNA copy of the DNA sequence:

" Hey, here is the place where you have to start your job of transcription". But what directs the Transcription factors in eukaryotic Cells to bind on the right place on the Genome to send the right signal?

DNA is wrapped around structural units called nucleosomes, acting as spools around which DNA winds. Without histones, the unwound DNA in chromosomes would be very long (a length to width ratio of more than 10 million to 1 in human DNA) Histones which compose the nucleosome are among the most conserved ( unchanged ) proteins known. Each nucleosome is a basic unit of DNA packaging in eukaryotes, consisting of a segment of DNA wound in sequence around eight histone protein cores. Histones are globular proteins with a flexible N-terminus (taken to be the tail) that protrudes from the nucleosome.  And these terminus tails are TRULY AMAZING. They contain a HISTONE CODE which DIRECTS GENE EXPRESSION !!

The critical concept of the histone code hypothesis is that the histone modifications serve to recruit other proteins by specific recognition of the modified histone via protein domains specialized for such purposes, rather than through simply stabilizing or destabilizing the interaction between histone and the underlying DNA. These recruited proteins then act to alter chromatin structure actively or to promote transcription.

The hypothesis is that chromatin-DNA interactions are guided by combinations of histone modifications.  There are a large number of different histone post-translational modifications (PTMs). These modifications are due through

methylation
ubiquitination
SUMOylation
crotonylation
butyrylation
propionylation of lysine residues
methylation
citrullination  
ADP-ribosylation of arginine residues
phosphorylation
glycosylation of serine and threonine residues

and alter chromatin structure. These Post-translational modifications (PTMs) of histones provide a fine-tuned mechanism for regulating chromatin structure and dynamics.

Histone post-translational modifications (PTMs) generate a COMPLEX COMBINATORIAL CODE  that regulates gene expression and nuclear functions, and whose deregulation has been documented in different types of cancers.

Davidson, one of the best known researchers in the field,  notes that, once established, the complexity of the dGRNs as integrated circuits makes them stubbornly resistant to mutational change—a point he has stressed in nearly every publication on the topic over the past fifteen years. "In the sea urchin embryo," he points out, "disarming any one of  these subcircuits produces some abnormality in expression."  Developmental gene regulatory networks resist mutational change because they are organized hierarchically. This means that some developmental gene regulatory networks control other gene regulatory networks, while some influence only the individual genes and proteins under their control. At the center of this regulatory hierarchy are the regulatory networks that specify the axis and global form of the animal body plan during development. These dGRNs cannot vary without causing catastrophic effects to the organism.

This raises the question: How could such a combinatorial code have evolved, if regulation is a must, and deregulation is a source of cancer and cell death?

Histones, which represent the protein component of chromatin, are site of many dynamic and reversible post-translational modifications that play a fundamental role in the regulation of the underlying genes. There is an ever-growing list of these modifications and the complexity of their action is only just beginning to be understood. However, it is clear that histone modifications play fundamental roles in most biological processes that are involved in the manipulation and expression of DNA.

This finding has DRAMATIC significance on the whole paradigm of evolution.

The histone Code is established through post-translational modifications on the histone tail, which direct proteins to bind on the right place at the right time on genes, and so, instruct the translation machinery to begin its job. These events are FINELY REGULATED AND FINE-TUNED, and when the Cell fails on this, the result is CANCER.

Question: Who or what directs, constructs implements the organizational rules and network design and critical finely tuned structural patterns and principles, directs the working in groups of transcription regulators, storing the histone code information, has found solutions to functional needs, organized, engineered and implemented the architecture, implemented the underlying autoregulatory circuits and feedback  regulation systems, ON and OFF switch states to activate or repress gene expression, making the whole system resistant to perturbations, feedforward loops (FFLs), and regulates the gene regulatory network through enzymes ?

Evolution, or design ? You are the judge.

Control of Gene Expression, and gene regulatory networks  point to intelligent design
http://reasonandscience.catsboard.com/t2194-control-of-gene-expression-and-gene-regulatory-networks-point-to-intelligent-design

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Origin of histones and nucleosomes in Eukaryotic Cells, how is best explained, by evolution, or design?

Evolution is proposed as a mechanism to create an increase of complexity of organisms. Supposedly there was a transition from simpler, prokaryotic Cells to Eukaryotic Cells. The common explanation is the endosymbiotic theory, but the following case, this has no importance.  While eukaryotes wrap their DNA around proteins called histones to help package the DNA into smaller spaces, most prokaryotes do not have histone proteins.

So how could that transition and the setup of nucleosomes and the make of histones have occurred?  

DNA in chromatin is organized in arrays of nucleosomes. Two copies of each histone protein, H2A, H2B, H3 and H4, are assembled into an octamer.  The nucleosome, in its role as the principal packaging element of DNA within the nucleus, is the primary determinant of DNA accessibility.

Dr. Stephen C. Meyer in his 1996 essay The Origin of Life and the Death of Materialism, wrote that "the information storage density of DNA, thanks in part to nucleosome spooling, is several trillion times that of our most advanced computer chips  So not only is there real information stored in DNA, but it is stored at a density on a molecular level, we can’t even approach with our best computers.

Bruce Alberts writes in his landmark book: " The molecular biology of the Cell"
The amino acid sequence of histone H4 from a pea differs from that of a cow at only 2 of the 102 positions. This strong evolutionary conservation suggests that the functions of histones involve nearly all of their amino acids so that a change in any position is deleterious to the cell. 


Another source reports that: As might be expected, most changes in histone sequences are lethal; the few that are not lethal cause changes in the normal pattern of gene expression, as well as other abnormalities.

If a change in histone sequences are lethal, how could it probably come to be in gradual steps, or trial and error? As long as the correct sequence is not reached, no function.....

Nucleosome assembly following DNA replication, DNA repair and gene transcription is critical for the maintenance of genome stability and epigenetic information.

This rises immediately the pertinent question, which Alberts, a rusted believer in evolution, avoids to ask: How could histones have evolved, if their specificity is essential, and less than the existent - about 100 amino acids - would not do the job, but, as the author admits "  the functions of histones involve nearly all of their amino acids " ? Is that not an implicit admittance of irreducible complexity?

The interface between DNA and histone is extensive: 142 hydrogen bonds are formed between DNA and the histone core in each nucleosome. Nearly half of these bonds form between the amino acid backbone of the histones and the phosphodiester backbone of the DNA.  More than one-fifth of the amino acids in each of the core histones are either lysine or arginine (two amino acids with basic side chains), and their positive charges can effectively neutralize the negatively charged DNA backbone. These numerous interactions explain in part why DNA of virtually any sequence can be bound on a histone octamer core. The sequence preference of nucleosomes must be weak enough to allow other factors to dominate, inasmuch as nucleosomes can occupy any one of a number of positions relative to the DNA sequence in most chromosomal regions.

What would happen if the net charge of histones would not neutralize the charge of the DNA backbone? DNA would bind in such a strong manner, that other factors would be unable to unwind the DNA, it could not be read, and effectively, the Cell would die. How could and would evolution find in a vast sequence space the right amino acids, providing the forces that permit the unwinding? Trial and error? Each time, it would try a sequence which is non-functional, the Cell would die. That makes the proposal of evolution as extremely unlikely. The histones had to be fully operational right from the beginning, what demonstrates that design is a far better and more case-adequate explanation rather than nonguided selective forces of evolution. 

There is more:

Nucleosomes must dynamically change so that DNA binding complexes can access their binding sites. These dynamic changes, which include nucleosome unwrapping, rewrapping, sliding, assembly, and disassembly, involve the formation and/or disruption of interactions within the interfaces between the DNA, H3/H4, and H2A/H2B components of the nucleosome. Histone protein tails are critical for controlling gene expression: they are dynamically modified by post-translational modifications (PTMs) many of the modifications have been correlated with regulatory cellular processes and chromatin structure.

A book cannot be found amongst thousands, or millions of books, in a library, unless there is an organization through a library management program which is necessary for the fast retrieval and return of books. The fast retrieval of information where to find a book in a library depends on the organized labeling of each library section, shelf, and eventually even the individual books, and is ordered in theme and genre sections, and every shelf has a tag which can be recognized and informs what books are there, and what themes. The books need first to be separated by genre and put together in categories. Then they have to be cataloged, one by one, before put together to the right shelf.

Histone protein tails are critical for controlling gene expression since they are like a computer which stores a library management program, containing, for example, the instruction: " its time to unwrap the DNA section of this histone, and express the DNA blueprint ". If the Cell cannot perform that critical information extraction at the right place, and the right time, the Cell is non-functional. Its a failure in its entirety. A factory cannot be built, unless the engineers know where and how to find the blueprints to build it. Reader proteins scan the histone tail, and signal to transcription factors and the transcription machinery: Come here, begin your job !! There is a large number of Histone tail  reader proteins which can read, "understand", and pass information on, but if just ONE of them is missing, like "histone acetyltransferase" (HAT), there would be no eukaryotic life !!  

Histone acetylation and deacetylation are essential parts of gene regulation, and crucial for life.  
Histone acetylation and deacetylation are the processes by which the lysine residues within the N-terminal tail protruding from the histone core of the nucleosome are acetylated and deacetylated as part of gene regulation.  Acetyl is a moiety ( a part of a molecule), and the introduction of an acetyl group into a molecule is called acetylation.  Acetylation removes the positive charge on the histones, thereby decreasing the interaction of the N termini of histones with the negatively charged phosphate groups of DNA. As a consequence, the condensed chromatin is transformed into a more relaxed structure that is associated with greater levels of gene transcription.

The make of histones is an engineering marvel.

Nucleosome assembly
Nucleosome assembly following DNA replication, DNA repair, and gene transcription is critical for the maintenance of genome stability and epigenetic information. Nucleosomes are assembled via replication-coupled or replication-independent pathways with the aid of histone chaperone proteins.

The sequence of correct histone octamer assembly is a multistep process, requiring several sequential folds and steps in a highly organized and precise manner, and must have been fully functional right from the beginning. The right process and sequence had to be programmed. The presence of histone chaperone proteins, which are specific, and could not have been co-opted from other systems, are essential. Histone chaperones promote chromatin assembly, disassembly and histone exchange to facilitate DNA replication, repair, and transcription. It's not feasible that they arose in a stepwise fashion, no function would be granted unless they were fully developed to exercise its specific function.


So we can conclude that all these parts, DNA,  Linker histone H1, histones H2A, H2B, H3 and H4,  acetyltransferases (HATs) and Histone deacetylase ( HDAC ) and the Histone Code  form a  set of well-matched, mutually interacting, nonarbitrarily individuated parts such that each part in the set is indispensable to maintaining the system's basic, and therefore original, function.  The set of these indispensable parts is known as the irreducible core of the system, while Histone chaperones are also essential to build the since they guide the process and each step along the assembly pathway.



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